1,045 Matching Annotations

Feb 2021
jmg.bmj.com jmg.bmj.com

Blood functional assay for rapid clinical interpretation of germline TP53 variants

43
1. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.792_794del p.(Leu265del)
  
  CGType:Variant Variant:42 CAID:CA645588451
2. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.393_395del p.(Asn131del)
  
  CGType:Variant Variant:17 ClinVarID:246343 CAID:CA10584593
3. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.323_325del p.(Gly108_Phe109delinsVal)
  
  CGType:Variant Variant:12 CAID:CA1139768485
4. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.1054G>T p.(Asp352Tyr)
  
  CGType:Variant Variant:7 ClinVarID:481148 CAID:CA397832246
5. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.1043T>C p.(Leu348Ser)
  
  CGType:Variant Variant:6 CAID:CA397832401
6. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.847C>T p.(Arg283Cys)
  
  CGType:Variant Variant:48 ClinVarID:127824 CAID:CA000457
7. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.833C>G p.(Pro278Arg)
  
  CGType:Variant Variant:45 ClinVarID:376644 CAID:CA16603061
8. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.329G>A p.(Arg110His)
  
  CGType:Variant Variant:15 ClinVarID:127808 CAID:CA000123
9. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.472C>T p.(Arg158Cys)
  
  CGType:Variant Variant:20 ClinVarID:127812 CAID:CA000225
10. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.402T>G p.(Phe134Leu)
  
  CGType:Variant Variant:18 CAID:CA397842793
11. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.723del p.(Cys242Alafs*5)
  
  CGType:Variant Variant:36 CAID:CA497717451
12. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.314G>A p.(Gly105Asp)
  
  CGType:Variant Variant:10 ClinVarID:141114 CAID:CA000102
13. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.215C>A p.(Pro72His)
  
  CGType:Variant Variant:8 ClinVarID:185120 CAID:CA000071
14. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.704A>G p.(Asn235Ser)
  
  CGType:Variant Variant:35 ClinVarID:127821 CAID:CA000343
15. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.770del p.(Leu257Argfs*88)
  
  CGType:Variant Variant:41 CAID:CA1139768484
16. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.375G>A p.?
  
  CGType:Variant Variant:16 ClinVarID:177825 CAID:CA000144
17. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.542G>A p.(Arg181His)
  
  CGType:Variant Variant:25 ClinVarID:142320 CAID:CA000259
18. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.1010G>A p.(Arg337His)
  
  CGType:Variant Variant:5 ClinVarID:12379 CAID:CA000013
19. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.910A>G p.(Thr304Ala)
  
  CGType:Variant Variant:51 ClinVarID:142702 CAID:CA000493
20. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.904G>A p.(Gly302Arg)
  
  CGType:Variant Variant:50 CAID:CA397836336
21. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.455del p.(Pro152Argfs*18)
  
  CGType:Variant Variant:19 ClinVarID:634779 CAID:CA497925664
22. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.869G>A p.(Arg290His)
  
  CGType:Variant Variant:49 ClinVarID:127825 CAID:CA000468
23. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.845G>C p.(Arg282Pro)
  
  CGType:Variant Variant:47 ClinVarID:376659 CAID:CA16603074
24. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.685T>C p.(Cys229Arg)
  
  CGType:Variant Variant:33 ClinVarID:420137 CAID:CA16620623
25. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.646G>A p.(Val216Met)
  
  CGType:Variant Variant:31 ClinVarID:182965 CAID:CA000308
26. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.578A>C p.(His193Pro)
  
  CGType:Variant Variant:28 ClinVarID:376612 CAID:CA16603033
27. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.577C>G p.(His193Asp)
  
  CGType:Variant Variant:27 ClinVarID:376613 CAID:CA16603034
28. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.523C>G p.(Arg175Gly)
  
  CGType:Variant Variant:22 ClinVarID:376649 CAID:CA16603066
29. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.323G>A p.(Gly108Asp)
  
  CGType:Variant Variant:14 CAID:CA397844631
30. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.31G>C p.(Glu11Gln)
  
  CGType:Variant Variant:11 ClinVarID:41723 CAID:CA000106
31. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.820del p.(Val274Phefs*71)
  
  CGType:Variant Variant:44 CAID:CA497716198
32. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.690del p.(Thr231Profs*16)
  
  CGType:Variant Variant:34 CAID:CA645588668
33. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.673-2A>G p.?
  
  CGType:Variant Variant:32 ClinVarID:458555 CAID:CA397839547
34. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.632_641del p.(Thr211Ilefs*33)
  
  CGType:Variant Variant:29 CAID:CA1139768487
35. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.491_494del p.(Lys164Serfs*5)
  
  CGType:Variant Variant:21 CAID:CA645588993
36. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.742C>T p.(Arg248Trp)
  
  CGType:Variant Variant:38 ClinVarID:12347 CAID:CA000382
37. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.323_329dup p.(Leu111Phefs*40)
  
  CGType:Variant Variant:13 ClinVarID:428860 CAID:CA645369686
38. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.216dup p.(Val73Argfs*76)
  
  CGType:Variant Variant:9 ClinVarID:182957 CAID:CA000073
39. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.818G>A p.(Arg273His)
  
  CGType:Variant Variant:43 ClinVarID:12366 CAID:CA000434
40. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.743G>A p.(Arg248Gln)
  
  CGType:Variant Variant:39 ClinVarID:12356 CAID:CA000387
41. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM_000546.5:c.524G>A p.(Arg175His)
  
  CGType:Variant Variant:23 ClinVarID:12374 CAID:CA000251
42. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  Supplemental material
  
  AssayResult: 52
  
  AssayResultAssertion: Abnormal
  
  Comment: See Table S3 for details; The blood sample used to test this variant was derived from an individual carrying the c.723del variant in combination with the c.*1175A>C variant in heterozygosity.
  
  CGType:FunctionalAssayResult FuncAssay:4 Variant:36 CAID:CA497717451
43. shannon_mcnulty 24 Feb 2021
  
  in Public
  
  We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.
  
  HGVS: NM000546.5:c.(?-202)(*1207?)del p.?
  
  Comment: A CAID could not be generated for this deletion variant with uncertain breakpoints.
  
  CGType:Variant Variant:2
Visit annotations in context

Tags

Variant:51

CGType:Variant

Variant:43

Variant:45

ClinVarID:182965

CAID:CA16603066

ClinVarID:12356

Variant:48

CAID:CA397832246

ClinVarID:376649

ClinVarID:12379

ClinVarID:142320

CAID:CA397844631

CAID:CA000144

Variant:21

CAID:CA000308

CAID:CA497716198

ClinVarID:127825

Variant:15

Variant:18

CAID:CA397832401

ClinVarID:142702

Variant:10

Variant:16

CAID:CA1139768484

Variant:34

CAID:CA000457

Variant:32

CGType:FunctionalAssayResult

ClinVarID:127808

Variant:5

CAID:CA397836336

CAID:CA645588668

ClinVarID:481148

ClinVarID:634779

CAID:CA645369686

Variant:42

ClinVarID:428860

FuncAssay:4

ClinVarID:420137

Variant:44

Variant:39

CAID:CA000468

Variant:28

Variant:17

ClinVarID:185120

Variant:22

CAID:CA000382

CAID:CA000434

ClinVarID:246343

CAID:CA397839547

CAID:CA497925664

Variant:25

Variant:13

CAID:CA000493

CAID:CA000123

CAID:CA497717451

ClinVarID:127812

CAID:CA000343

CAID:CA000251

CAID:CA000225

CAID:CA645588993

CAID:CA16603061

CAID:CA397842793

ClinVarID:12347

Variant:20

Variant:41

ClinVarID:182957

CAID:CA10584593

ClinVarID:376612

ClinVarID:376644

Variant:9

Variant:7

Variant:6

CAID:CA000073

CAID:CA645588451

Variant:33

Variant:49

Variant:36

ClinVarID:127824

CAID:CA000102

CAID:CA000071

CAID:CA16603034

Variant:27

ClinVarID:376613

Variant:11

CAID:CA000259

Variant:38

CAID:CA1139768485

Variant:31

Variant:12

CAID:CA16620623

ClinVarID:41723

Variant:35

Variant:8

ClinVarID:458555

CAID:CA16603074

ClinVarID:12366

ClinVarID:12374

CAID:CA000106

Variant:19

Variant:50

ClinVarID:177825

Variant:14

Variant:23

Variant:29

CAID:CA000387

ClinVarID:376659

CAID:CA16603033

Variant:2

Variant:47

ClinVarID:141114

CAID:CA000013

ClinVarID:127821

CAID:CA1139768487

Annotators

shannon_mcnulty

URL

jmg.bmj.com/content/early/2020/10/13/jmedgenet-2020-107059
Jan 2019
journals.plos.org journals.plos.org

A Novel Splice-Site Mutation in the GJB2 Gene Causing Mild Postlingual Hearing Impairment

1
1. shannon_mcnulty 23 Jan 2019
  
  in Public
  
  The 313-bp product suggested the existence of a second alternative acceptor site (see below). Overall, in subject II:4, the amount of transcripts originating from the c. -22-2A>C allele was markedly inferior to that of transcripts from the c.35delG allele
  
  Alternative acceptor splice site identifiedby RT-qPCR
Visit annotations in context

Annotators

shannon_mcnulty

URL

journals.plos.org/plosone/article
Local file Local file

Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss

1
1. shannon_mcnulty 22 Jan 2019
  
  in Public
  
  Upon specifying the ACMG/AMP rules,conferencecallsandemailcorrespondencewereusedforthevariantpilotusingasetof51variantsfromninecommonHLgenesthatrepre-sentthevariedinheritancepatterns,evidencetypes,andphenotypicspectrumseenacrossHLcohorts(seeVariantPilotmethodsbelow).ThefinalsetofspecifiedrulesisshowninTable1.
  
  Variant selection for pilot
Annotators

shannon_mcnulty

shannon_mcnulty

Annotations: 1,045

Joined: January 7, 2019

Tags

Annotators

URL

Annotators

URL

Annotators