rs6785930

Positions:

Variant summary

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

The NM_022788.5(P2RY12):c.18C>T(p.Asn6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,610,536 control chromosomes in the GnomAD database, including 74,988 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 5847 hom., cov: 31)

Exomes 𝑓: 0.31 ( 69141 hom. )

Consequence

P2RY12
NM_022788.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.08

Variant links:

Genes affected

P2RY12 (HGNC:18124): (purinergic receptor P2Y12) The product of this gene belongs to the family of G-protein coupled receptors. This family has several receptor subtypes with different pharmacological selectivity, which overlaps in some cases, for various adenosine and uridine nucleotides. This receptor is involved in platelet aggregation, and is a potential target for the treatment of thromboembolisms and other clotting disorders. Mutations in this gene are implicated in bleeding disorder, platelet type 8 (BDPLT8). Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

P2RY12 links:

MED12L (HGNC:16050): (mediator complex subunit 12L) The protein encoded by this gene is part of the Mediator complex, which is involved in transcriptional coactivation of nearly all RNA polymerase II-dependent genes. The Mediator complex links gene-specific transcriptional activators with the basal transcription machinery. [provided by RefSeq, May 2010]

MED12L 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=-0.51).

BP6

Variant 3-151338828-G-A is Benign according to our data. Variant chr3-151338828-G-A is described in ClinVar as [Benign]. Clinvar id is 261632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.08 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RY12	NM_022788.5 linkuse as main transcript	c.18C>T	p.Asn6=	synonymous_variant	3/3	ENST00000302632.4
MED12L	NM_001393769.1 linkuse as main transcript	c.2251-11231G>A		intron_variant		ENST00000687756.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RY12	ENST00000302632.4 linkuse as main transcript	c.18C>T	p.Asn6=	synonymous_variant	3/3	1	NM_022788.5	P1
MED12L	ENST00000687756.1 linkuse as main transcript	c.2251-11231G>A		intron_variant			NM_001393769.1	A2

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41154

AN:

151804

Hom.:

5848

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.278

GnomAD3 exomes

AF:

0.295

AC:

73921

AN:

250832

Hom.:

11317

AF XY:

0.296

AC XY:

40174

AN XY:

135570

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.322

Gnomad ASJ exome

AF:

0.197

Gnomad EAS exome

AF:

0.228

Gnomad SAS exome

AF:

0.294

Gnomad FIN exome

AF:

0.369

Gnomad NFE exome

AF:

0.307

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.305

AC:

445058

AN:

1458612

Hom.:

69141

Cov.:

AF XY:

0.306

AC XY:

221828

AN XY:

725744

show subpopulations

Gnomad4 AFR exome

AF:

0.175

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.198

Gnomad4 EAS exome

AF:

0.240

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.368

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.290

GnomAD4 genome

AF:

0.271

AC:

41170

AN:

151924

Hom.:

5847

Cov.:

AF XY:

0.273

AC XY:

20291

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.195

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.302

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.310

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.286

Hom.:

3825

Bravo

AF:

0.259

Asia WGS

AF:

0.245

AC:

852

AN:

3478

EpiCase

AF:

0.300

EpiControl

AF:

0.296

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

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

-0.51

CADD

Benign

3.9

DANN

Benign

0.69

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