12-116148609-CTATATATATA-CTATATATA

Position:

• chr12-116148609-CTATATATATA-CTATATATA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015335.5(MED13L):​c.311-37099_311-37098delTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 180,914 control chromosomes in the GnomAD database, including 7,381 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (7256 hom., cov: 0)
  • Exomes 𝑓: 0.25 (125 hom.)
• Consequence: MED13L NM_015335.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

MED13L (HGNC:22962): (mediator complex subunit 13L) The protein encoded by this gene is a subunit of the Mediator complex, a large complex of proteins that functions as a transcriptional coactivator for most RNA polymerase II-transcribed genes. The encoded protein is involved in early development of the heart and brain. Defects in this gene are a cause of transposition of the great arteries, dextro-looped (DTGA).[provided by RefSeq, Jul 2010]

MIR620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MED13L	NM_015335.5	c.311-37099_311-37098delTA		intron_variant		ENST00000281928.9	NP_056150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MED13L	ENST00000281928.9	c.311-37099_311-37098delTA		intron_variant		1	NM_015335.5	ENSP00000281928.3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 44887 AN: 143214 Hom.: 7259 Cov.: 0

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.285

GnomAD3 exomes AF: 0.299 AC: 9420 AN: 31506 Hom.: 119 AF XY: 0.306 AC XY: 5296 AN XY: 17292

Gnomad AFR exome AF: 0.303

Gnomad AMR exome AF: 0.374

Gnomad ASJ exome AF: 0.284

Gnomad EAS exome AF: 0.401

Gnomad SAS exome AF: 0.387

Gnomad FIN exome AF: 0.258

Gnomad NFE exome AF: 0.291

Gnomad OTH exome AF: 0.279

GnomAD4 exome AF: 0.252 AC: 9514 AN: 37682 Hom.: 125 AF XY: 0.258 AC XY: 5625 AN XY: 21834

Gnomad4 AFR exome AF: 0.348

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.254

Gnomad4 EAS exome AF: 0.281

Gnomad4 SAS exome AF: 0.343

Gnomad4 FIN exome AF: 0.228

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.262

GnomAD4 genome AF: 0.313 AC: 44893 AN: 143232 Hom.: 7256 Cov.: 0 AF XY: 0.318 AC XY: 22100 AN XY: 69598

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3043743; hg19: chr12-116586414;