Variant rs5030705 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.507G>A(p.Thr169Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,611,158 control chromosomes in the GnomAD database, including 32,180 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2270 hom., cov: 34)

Exomes 𝑓: 0.19 ( 29910 hom. )

Consequence

GP6
NM_001083899.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.85

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 19-55027681-C-T is Benign according to our data. Variant chr19-55027681-C-T is described in ClinVar as [Benign]. Clinvar id is 257420.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.85 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GP6	NM_001083899.2 linkuse as main transcript	c.507G>A	p.Thr169Thr	synonymous_variant	4/8	ENST00000310373.7	NP_001077368.2	Q9HCN6-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GP6	ENST00000310373.7 linkuse as main transcript	c.507G>A	p.Thr169Thr	synonymous_variant	4/8	1	NM_001083899.2	ENSP00000308782.3		Q9HCN6-3
GP6	ENST00000417454.5 linkuse as main transcript	c.507G>A	p.Thr169Thr	synonymous_variant	4/8	1		ENSP00000394922.1		Q9HCN6-1

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22215

AN:

152118

Hom.:

2270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0410

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.0976

Gnomad EAS

AF:

0.0268

Gnomad SAS

AF:

0.0515

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.146

GnomAD3 exomes

AF:

0.148

AC:

36815

AN:

249498

Hom.:

3600

AF XY:

0.148

AC XY:

20026

AN XY:

135390

show subpopulations

Gnomad AFR exome

AF:

0.0377

Gnomad AMR exome

AF:

0.0867

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.0262

Gnomad SAS exome

AF:

0.0602

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.208

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.192

AC:

280838

AN:

1458922

Hom.:

29910

Cov.:

AF XY:

0.189

AC XY:

137384

AN XY:

726042

show subpopulations

Gnomad4 AFR exome

AF:

0.0350

Gnomad4 AMR exome

AF:

0.0907

Gnomad4 ASJ exome

AF:

0.0999

Gnomad4 EAS exome

AF:

0.0368

Gnomad4 SAS exome

AF:

0.0613

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.219

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.146

AC:

22205

AN:

152236

Hom.:

2270

Cov.:

AF XY:

0.145

AC XY:

10774

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0409

Gnomad4 AMR

AF:

0.127

Gnomad4 ASJ

AF:

0.0976

Gnomad4 EAS

AF:

0.0263

Gnomad4 SAS

AF:

0.0516

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.183

Hom.:

1436

Bravo

AF:

0.132

Asia WGS

AF:

0.0430

AC:

150

AN:

3478

EpiCase

AF:

0.198

EpiControl

AF:

0.202

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.088

DANN

Benign

0.92

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