19-55027704-T-G

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001083899.2(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_001083899.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.191

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 made for transcript

Verdict is Benign. Variant got -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 id is 257418.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-55027704-T-G is described in Lovd as [Benign].

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GP6	NM_001083899.2 link	c.484A>C	p.Arg162Arg	synonymous_variant	Exon 4 of 8	ENST00000310373.7	NP_001077368.2	Q9HCN6-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GP6	ENST00000310373.7 link	c.484A>C	p.Arg162Arg	synonymous_variant	Exon 4 of 8	1	NM_001083899.2	ENSP00000308782.3		Q9HCN6-3
GP6	ENST00000417454.5 link	c.484A>C	p.Arg162Arg	synonymous_variant	Exon 4 of 8	1		ENSP00000394922.1		Q9HCN6-1

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

GnomAD3 exomes

AF:

0.853

AC:

212976

AN:

249534

Hom.:

91456

AF XY:

0.848

AC XY:

114776

AN XY:

135400

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 SAS exome

AF:

0.787

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

Gnomad4 AFR exome

AF:

0.764

Gnomad4 AMR exome

AF:

0.923

Gnomad4 ASJ exome

AF:

0.795

Gnomad4 EAS exome

AF:

0.981

Gnomad4 SAS exome

AF:

0.789

Gnomad4 FIN exome

AF:

0.883

Gnomad4 NFE exome

AF:

0.838

Gnomad4 OTH exome

AF:

0.839

GnomAD4 genome

AF:

0.834

AC:

126953

AN:

152188

Hom.:

53186

Cov.:

AF XY:

0.838

AC XY:

62397

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.773

Gnomad4 AMR

AF:

0.887

Gnomad4 ASJ

AF:

0.795

Gnomad4 EAS

AF:

0.976

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.890

Gnomad4 NFE

AF:

0.846

Gnomad4 OTH

AF:

0.846

Alfa

AF:

0.833

Hom.:

32464

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

- -

Nov 12, 2018

GeneDx

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

- -

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.3

DANN

Benign

0.78

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over