3-151250075-C-T

Variant names:

• chr3-151250075-C-T
• rs3846072
• NM_001393769.1:c.2250+56409C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393769.1(MED12L):​c.2250+56409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,914 control chromosomes in the GnomAD database, including 16,726 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 0.46 (16726 hom., cov: 32)
• Consequence: MED12L NM_001393769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 1 publications found

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]

P2RY14 (HGNC:16442): (purinergic receptor P2Y14) The product of this gene belongs to the family of G-protein coupled receptors, which contains several receptor subtypes with different pharmacological selectivity for various adenosine and uridine nucleotides. This receptor is a P2Y purinergic receptor for UDP-glucose and other UDP-sugars coupled to G-proteins. It has been implicated in extending the known immune system functions of P2Y receptors by participating in the regulation of the stem cell compartment, and it may also play a role in neuroimmune function. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393769.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MED12L	NM_001393769.1	MANE Select	c.2250+56409C>T		intron	N/A	NP_001380698.1
	P2RY14	NM_014879.4	MANE Select	c.-133+28212G>A		intron	N/A	NP_055694.3
	MED12L	NM_053002.6		c.2145+56409C>T		intron	N/A	NP_443728.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MED12L	ENST00000687756.1	MANE Select	c.2250+56409C>T		intron	N/A	ENSP00000508695.1
	P2RY14	ENST00000309170.8	TSL:1 MANE Select	c.-133+28212G>A		intron	N/A	ENSP00000308361.3
	MED12L	ENST00000474524.5	TSL:1	c.2145+56409C>T		intron	N/A	ENSP00000417235.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69344 AN: 151796 Hom.: 16720 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.501

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.457 AC: 69374 AN: 151914 Hom.: 16726 Cov.: 32 AF XY: 0.461 AC XY: 34219 AN XY: 74274

African (AFR) AF: 0.287 AC: 11897 AN: 41422

American (AMR) AF: 0.521 AC: 7941 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3100 AN: 5164

South Asian (SAS) AF: 0.575 AC: 2765 AN: 4812

European-Finnish (FIN) AF: 0.483 AC: 5100 AN: 10564

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34770 AN: 67920

Other (OTH) AF: 0.500 AC: 1051 AN: 2104

Alfa AF: 0.488 Hom.: 7238

Bravo AF: 0.452

Asia WGS AF: 0.535 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3846072; hg19: chr3-150967863;