Variant rs1671151 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001083899.2(GP6):c.1419C>T(p.Pro473=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 1,613,356 control chromosomes in the GnomAD database, including 525,252 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 43534 hom., cov: 31)

Exomes 𝑓: 0.81 ( 481718 hom. )

Consequence

GP6
NM_001083899.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.125

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:

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=-0.88).

BP6

Variant 19-55014526-G-A is Benign according to our data. Variant chr19-55014526-G-A is described in ClinVar as [Benign]. Clinvar id is 257411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-55014526-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.125 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GP6	NM_001083899.2 linkuse as main transcript	c.1419C>T	p.Pro473=	synonymous_variant	8/8	ENST00000310373.7
GP6-AS1	XR_001754012.3 linkuse as main transcript	n.121+8062G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GP6	ENST00000310373.7 linkuse as main transcript	c.1419C>T	p.Pro473=	synonymous_variant	8/8	1	NM_001083899.2		Q9HCN6-3
GP6-AS1	ENST00000593060.5 linkuse as main transcript	n.155+8062G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113202

AN:

151980

Hom.:

43529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.799

Gnomad ASJ

AF:

0.792

Gnomad EAS

AF:

0.825

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.876

Gnomad MID

AF:

0.841

Gnomad NFE

AF:

0.832

Gnomad OTH

AF:

0.785

GnomAD3 exomes

AF:

0.798

AC:

199147

AN:

249524

Hom.:

80479

AF XY:

0.798

AC XY:

108007

AN XY:

135372

show subpopulations

Gnomad AFR exome

AF:

0.518

Gnomad AMR exome

AF:

0.830

Gnomad ASJ exome

AF:

0.797

Gnomad EAS exome

AF:

0.837

Gnomad SAS exome

AF:

0.728

Gnomad FIN exome

AF:

0.871

Gnomad NFE exome

AF:

0.825

Gnomad OTH exome

AF:

0.810

GnomAD4 exome

AF:

0.810

AC:

1183777

AN:

1461258

Hom.:

481718

Cov.:

AF XY:

0.809

AC XY:

588445

AN XY:

726954

show subpopulations

Gnomad4 AFR exome

AF:

0.524

Gnomad4 AMR exome

AF:

0.826

Gnomad4 ASJ exome

AF:

0.795

Gnomad4 EAS exome

AF:

0.809

Gnomad4 SAS exome

AF:

0.732

Gnomad4 FIN exome

AF:

0.871

Gnomad4 NFE exome

AF:

0.822

Gnomad4 OTH exome

AF:

0.798

GnomAD4 genome

AF:

0.745

AC:

113250

AN:

152098

Hom.:

43534

Cov.:

AF XY:

0.748

AC XY:

55626

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.533

Gnomad4 AMR

AF:

0.799

Gnomad4 ASJ

AF:

0.792

Gnomad4 EAS

AF:

0.824

Gnomad4 SAS

AF:

0.722

Gnomad4 FIN

AF:

0.876

Gnomad4 NFE

AF:

0.832

Gnomad4 OTH

AF:

0.782

Alfa

AF:

0.810

Hom.:

87611

Bravo

AF:

0.731

Asia WGS

AF:

0.751

AC:

2612

AN:

3478

EpiCase

AF:

0.825

EpiControl

AF:

0.826

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Platelet-type bleeding disorder 11

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

DANN

Benign

0.50

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