rs10935838

Positions:

• chr3-151340459-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393769.1(MED12L):​c.2251-9600A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,590 control chromosomes in the GnomAD database, including 54,971 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.85 (54834 hom., cov: 33)
  • Exomes 𝑓: 0.83 (137 hom.)
• Consequence: MED12L NM_001393769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

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]

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MED12L	NM_001393769.1	c.2251-9600A>G		intron_variant		ENST00000687756.1	NP_001380698.1
P2RY12	NM_022788.5	c.-15+137T>C		intron_variant		ENST00000302632.4	NP_073625.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P2RY12	ENST00000302632.4	c.-15+137T>C		intron_variant		1	NM_022788.5	ENSP00000307259	P1
MED12L	ENST00000687756.1	c.2251-9600A>G		intron_variant			NM_001393769.1	ENSP00000508695	A2

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129060 AN: 152076 Hom.: 54804 Cov.: 33

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.880

GnomAD4 exome AF: 0.833 AC: 330 AN: 396 Hom.: 137 AF XY: 0.825 AC XY: 203 AN XY: 246

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.849 AC: 129144 AN: 152194 Hom.: 54834 Cov.: 33 AF XY: 0.851 AC XY: 63321 AN XY: 74410

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.874

Alfa AF: 0.842 Hom.: 16502

Bravo AF: 0.850

Asia WGS AF: 0.837 AC: 2905 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.42
DANN	Benign	0.57

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

Other links and lift over

dbSNP: rs10935838; hg19: chr3-151058247;