rs5030705

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

13 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 -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 VariationId 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 rank	MANE	Protein	UniProt
GP6	NM_001083899.2 link	c.507G>A	p.Thr169Thr	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.507G>A	p.Thr169Thr	synonymous_variant	Exon 4 of 8	1	NM_001083899.2	ENSP00000308782.3		Q9HCN6-3
GP6	ENST00000417454.5 link	c.507G>A	p.Thr169Thr	synonymous_variant	Exon 4 of 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

GnomAD2 exomes

AF:

0.148

AC:

36815

AN:

249498

AF XY:

0.148

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 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

African (AFR)

AF:

0.0350

AC:

1172

AN:

33456

American (AMR)

AF:

0.0907

AC:

4057

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0999

AC:

2609

AN:

26128

East Asian (EAS)

AF:

0.0368

AC:

1461

AN:

39684

South Asian (SAS)

AF:

0.0613

AC:

5288

AN:

86222

European-Finnish (FIN)

AF:

0.244

AC:

12997

AN:

53374

Middle Eastern (MID)

AF:

0.0889

AC:

512

AN:

5762

European-Non Finnish (NFE)

AF:

0.219

AC:

242834

AN:

1109292

Other (OTH)

AF:

0.164

AC:

9908

AN:

60282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

12034

24068

36103

48137

60171

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8098

16196

24294

32392

40490

<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:

0.146

AC:

22205

AN:

152236

Hom.:

2270

Cov.:

AF XY:

0.145

AC XY:

10774

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0409

AC:

1699

AN:

41558

American (AMR)

AF:

0.127

AC:

1938

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0976

AC:

339

AN:

3472

East Asian (EAS)

AF:

0.0263

AC:

136

AN:

5174

South Asian (SAS)

AF:

0.0516

AC:

249

AN:

4830

European-Finnish (FIN)

AF:

0.236

AC:

2497

AN:

10594

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.218

AC:

14803

AN:

67996

Other (OTH)

AF:

0.144

AC:

303

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

915

1829

2744

3658

4573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.182

Hom.:

1440

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jun 09, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.088

(source)

DANN

Benign

0.92

PhyloP100

-1.9

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over