rs1671151

Variant names:

Your query was ambiguous. Multiple possible variants found:

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.1419C>T(p.Pro473Pro) 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:4

Conservation

PhyloP100: 0.125

Publications

24 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:

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=-0.88).

BP6

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

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 rank	MANE	Protein	UniProt
GP6	NM_001083899.2 link	c.1419C>T	p.Pro473Pro	synonymous_variant	Exon 8 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.1419C>T	p.Pro473Pro	synonymous_variant	Exon 8 of 8	1	NM_001083899.2	ENSP00000308782.3		Q9HCN6-3
GP6	ENST00000417454.5 link	c.*395C>T		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000394922.1		Q9HCN6-1

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

GnomAD2 exomes

AF:

0.798

AC:

199147

AN:

249524

AF XY:

0.798

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 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

African (AFR)

AF:

0.524

AC:

17520

AN:

33452

American (AMR)

AF:

0.826

AC:

36919

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.795

AC:

20781

AN:

26134

East Asian (EAS)

AF:

0.809

AC:

32108

AN:

39696

South Asian (SAS)

AF:

0.732

AC:

63147

AN:

86246

European-Finnish (FIN)

AF:

0.871

AC:

46527

AN:

53420

Middle Eastern (MID)

AF:

0.782

AC:

4511

AN:

5768

European-Non Finnish (NFE)

AF:

0.822

AC:

914115

AN:

1111448

Other (OTH)

AF:

0.798

AC:

48149

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

12831

25663

38494

51326

64157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20888

41776

62664

83552

104440

<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:

0.745

AC:

113250

AN:

152098

Hom.:

43534

Cov.:

AF XY:

0.748

AC XY:

55626

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.533

AC:

22101

AN:

41448

American (AMR)

AF:

0.799

AC:

12208

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.792

AC:

2749

AN:

3472

East Asian (EAS)

AF:

0.824

AC:

4261

AN:

5168

South Asian (SAS)

AF:

0.722

AC:

3477

AN:

4818

European-Finnish (FIN)

AF:

0.876

AC:

9293

AN:

10608

Middle Eastern (MID)

AF:

0.839

AC:

245

AN:

292

European-Non Finnish (NFE)

AF:

0.832

AC:

56565

AN:

68002

Other (OTH)

AF:

0.782

AC:

1654

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1364

2728

4093

5457

6821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.795

Hom.:

133458

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:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

- -

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

-0.88

CADD

Benign

2.0

(source)

DANN

Benign

0.50

PhyloP100

0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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