rs892089

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001083899.2(GP6):c.495T>C(p.Phe165Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 1,611,254 control chromosomes in the GnomAD database, including 521,271 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.76 ( 44637 hom., cov: 33)

Exomes 𝑓: 0.81 ( 476634 hom. )

Consequence

GP6
NM_001083899.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0460

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 19-55027693-A-G is Benign according to our data. Variant chr19-55027693-A-G is described in ClinVar as [Benign]. Clinvar id is 257419.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-55027693-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.046 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GP6	NM_001083899.2 link	c.495T>C	p.Phe165Phe	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.495T>C	p.Phe165Phe	synonymous_variant	Exon 4 of 8	1	NM_001083899.2	ENSP00000308782.3		Q9HCN6-3
GP6	ENST00000417454.5 link	c.495T>C	p.Phe165Phe	synonymous_variant	Exon 4 of 8	1		ENSP00000394922.1		Q9HCN6-1

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

115429

AN:

152002

Hom.:

44627

Cov.:

show subpopulations

Gnomad AFR

AF:

0.598

Gnomad AMI

AF:

0.770

Gnomad AMR

AF:

0.798

Gnomad ASJ

AF:

0.780

Gnomad EAS

AF:

0.822

Gnomad SAS

AF:

0.720

Gnomad FIN

AF:

0.875

Gnomad MID

AF:

0.842

Gnomad NFE

AF:

0.826

Gnomad OTH

AF:

0.790

GnomAD3 exomes

AF:

0.799

AC:

199303

AN:

249510

Hom.:

80307

AF XY:

0.798

AC XY:

107976

AN XY:

135390

show subpopulations

Gnomad AFR exome

AF:

0.586

Gnomad AMR exome

AF:

0.831

Gnomad ASJ exome

AF:

0.786

Gnomad EAS exome

AF:

0.835

Gnomad SAS exome

AF:

0.725

Gnomad FIN exome

AF:

0.870

Gnomad NFE exome

AF:

0.819

Gnomad OTH exome

AF:

0.805

GnomAD4 exome

AF:

0.807

AC:

1177329

AN:

1459134

Hom.:

476634

Cov.:

AF XY:

0.806

AC XY:

585307

AN XY:

726074

show subpopulations

Gnomad4 AFR exome

AF:

0.589

Gnomad4 AMR exome

AF:

0.826

Gnomad4 ASJ exome

AF:

0.782

Gnomad4 EAS exome

AF:

0.806

Gnomad4 SAS exome

AF:

0.730

Gnomad4 FIN exome

AF:

0.869

Gnomad4 NFE exome

AF:

0.817

Gnomad4 OTH exome

AF:

0.797

GnomAD4 genome

AF:

0.759

AC:

115485

AN:

152120

Hom.:

44637

Cov.:

AF XY:

0.764

AC XY:

56820

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.598

Gnomad4 AMR

AF:

0.798

Gnomad4 ASJ

AF:

0.780

Gnomad4 EAS

AF:

0.821

Gnomad4 SAS

AF:

0.719

Gnomad4 FIN

AF:

0.875

Gnomad4 NFE

AF:

0.826

Gnomad4 OTH

AF:

0.787

Alfa

AF:

0.789

Hom.:

22809

Bravo

AF:

0.747

Asia WGS

AF:

0.749

AC:

2607

AN:

3478

EpiCase

AF:

0.820

EpiControl

AF:

0.823

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

- -

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

- -

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

-0.87

CADD

Benign

4.9

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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