chr19-55027704-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016363.5(GP6):c.484A>C(p.Arg162Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 1,611,948 control chromosomes in the GnomAD database, including 570,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 53186 hom., cov: 33)

Exomes 𝑓: 0.84 ( 517130 hom. )

Consequence

GP6
NM_016363.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.191

Publications

25 publications found

Variant links:

Genes affected

GP6 (HGNC:14388): (glycoprotein VI platelet) This gene encodes a platelet membrane glycoprotein of the immunoglobulin superfamily. The encoded protein is a receptor for collagen and plays a critical role in collagen-induced platelet aggregation and thrombus formation. The encoded protein forms a complex with the Fc receptor gamma-chain that initiates the platelet activation signaling cascade upon collagen binding. Mutations in this gene are a cause of platelet-type bleeding disorder-11 (BDPLT11). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

GP6 links:

ENSG00000267149 (HGNC:):

ENSG00000267149 links:

GP6-AS1 (HGNC:55305): (GP6 antisense RNA 1)

GP6-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-55027704-T-G is Benign according to our data. Variant chr19-55027704-T-G is described in ClinVar as Benign. ClinVar VariationId is 257418.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016363.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GP6	NM_016363.5	MANE Select	c.484A>C	p.Arg162Arg	synonymous	Exon 4 of 8	NP_057447.5
GP6	NM_001083899.2		c.484A>C	p.Arg162Arg	synonymous	Exon 4 of 8	NP_001077368.2
GP6	NM_001256017.2		c.484A>C	p.Arg162Arg	synonymous	Exon 4 of 7	NP_001242946.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GP6	ENST00000417454.5	TSL:1 MANE Select	c.484A>C	p.Arg162Arg	synonymous	Exon 4 of 8	ENSP00000394922.1
GP6	ENST00000310373.7	TSL:1	c.484A>C	p.Arg162Arg	synonymous	Exon 4 of 8	ENSP00000308782.3
GP6	ENST00000333884.2	TSL:1	c.484A>C	p.Arg162Arg	synonymous	Exon 4 of 7	ENSP00000334552.2

Frequencies

GnomAD3 genomes

AF:

0.834

AC:

126867

AN:

152070

Hom.:

53160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.773

Gnomad AMI

AF:

0.770

Gnomad AMR

AF:

0.887

Gnomad ASJ

AF:

0.795

Gnomad EAS

AF:

0.976

Gnomad SAS

AF:

0.786

Gnomad FIN

AF:

0.890

Gnomad MID

AF:

0.848

Gnomad NFE

AF:

0.846

Gnomad OTH

AF:

0.847

GnomAD2 exomes

AF:

0.853

AC:

212976

AN:

249534

AF XY:

0.848

show subpopulations

Gnomad AFR exome

AF:

0.765

Gnomad AMR exome

AF:

0.927

Gnomad ASJ exome

AF:

0.800

Gnomad EAS exome

AF:

0.983

Gnomad FIN exome

AF:

0.884

Gnomad NFE exome

AF:

0.840

Gnomad OTH exome

AF:

0.843

GnomAD4 exome

AF:

0.841

AC:

1227329

AN:

1459760

Hom.:

517130

Cov.:

AF XY:

0.840

AC XY:

609910

AN XY:

726298

show subpopulations

African (AFR)

AF:

0.764

AC:

25577

AN:

33458

American (AMR)

AF:

0.923

AC:

41279

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.795

AC:

20769

AN:

26124

East Asian (EAS)

AF:

0.981

AC:

38952

AN:

39692

South Asian (SAS)

AF:

0.789

AC:

68039

AN:

86224

European-Finnish (FIN)

AF:

0.883

AC:

47122

AN:

53390

Middle Eastern (MID)

AF:

0.802

AC:

4619

AN:

5758

European-Non Finnish (NFE)

AF:

0.838

AC:

930344

AN:

1110068

Other (OTH)

AF:

0.839

AC:

50628

AN:

60322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

11120

22240

33361

44481

55601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21032

42064

63096

84128

105160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.834

AC:

126953

AN:

152188

Hom.:

53186

Cov.:

AF XY:

0.838

AC XY:

62397

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.773

AC:

32101

AN:

41524

American (AMR)

AF:

0.887

AC:

13570

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.795

AC:

2761

AN:

3472

East Asian (EAS)

AF:

0.976

AC:

5038

AN:

5164

South Asian (SAS)

AF:

0.786

AC:

3791

AN:

4826

European-Finnish (FIN)

AF:

0.890

AC:

9440

AN:

10604

Middle Eastern (MID)

AF:

0.850

AC:

250

AN:

294

European-Non Finnish (NFE)

AF:

0.846

AC:

57512

AN:

67986

Other (OTH)

AF:

0.846

AC:

1789

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1079

2158

3238

4317

5396

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.835

Hom.:

109260

Bravo

AF:

0.832

Asia WGS

AF:

0.885

AC:

3077

AN:

3478

EpiCase

AF:

0.839

EpiControl

AF:

0.841

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Platelet-type bleeding disorder 11

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.3

(source)

DANN

Benign

0.78

PhyloP100

0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over