rs12941827

chr17-61952616-C-G

Variant summary

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

The NM_005121.3(MED13):c.6117+349G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,144 control chromosomes in the GnomAD database, including 1,997 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 0.16 (1997 hom., cov: 32)
• Consequence: MED13 NM_005121.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

MED13 (HGNC:22474): (mediator complex subunit 13) This gene encodes a component of the mediator complex (also known as TRAP, SMCC, DRIP, or ARC), a transcriptional coactivator complex thought to be required for the expression of almost all genes. The mediator complex is recruited by transcriptional activators or nuclear receptors to induce gene expression, possibly by interacting with RNA polymerase II and promoting the formation of a transcriptional pre-initiation complex. The product of this gene is proposed to form a sub-complex with MED12, cyclin C, and CDK8 that can negatively regulate transactivation by mediator. [provided by RefSeq, Jul 2008]

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 (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MED13	NM_005121.3	c.6117+349G>C		intron_variant		ENST00000397786.7
MED13	XM_011525551.3	c.5958+349G>C		intron_variant
MED13	XM_011525553.4	c.5448+349G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MED13	ENST00000397786.7	c.6117+349G>C		intron_variant		1	NM_005121.3	P1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23778 AN: 152026 Hom.: 1999 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.0907

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.156 AC: 23779 AN: 152144 Hom.: 1997 Cov.: 32 AF XY: 0.151 AC XY: 11226 AN XY: 74392

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.0907

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.192

Alfa AF: 0.149 Hom.: 234

Bravo AF: 0.168

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.20
Dann	Benign	0.61

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: rs12941827; hg19: chr17-60029977;