12-116148609-CTATATATATA-CTATATA

Position:

• chr12-116148609-CTATATATATA-CTATATA

Variant summary

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

The NM_015335.5(MED13L):​c.311-37101_311-37098delTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 182,350 control chromosomes in the GnomAD database, including 3,348 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.20 (3016 hom., cov: 0)
  • Exomes 𝑓: 0.23 (332 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 (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MED13L	NM_015335.5	c.311-37101_311-37098delTATA		intron_variant		ENST00000281928.9	NP_056150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MED13L	ENST00000281928.9	c.311-37101_311-37098delTATA		intron_variant		1	NM_015335.5	ENSP00000281928.3

Frequencies

GnomAD3 genomes AF: 0.204 AC: 29198 AN: 143308 Hom.: 3016 Cov.: 0

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.218

GnomAD3 exomes AF: 0.241 AC: 7602 AN: 31506 Hom.: 259 AF XY: 0.239 AC XY: 4136 AN XY: 17292

Gnomad AFR exome AF: 0.231

Gnomad AMR exome AF: 0.199

Gnomad ASJ exome AF: 0.143

Gnomad EAS exome AF: 0.317

Gnomad SAS exome AF: 0.279

Gnomad FIN exome AF: 0.281

Gnomad NFE exome AF: 0.214

Gnomad OTH exome AF: 0.218

GnomAD4 exome AF: 0.229 AC: 8944 AN: 39024 Hom.: 332 AF XY: 0.232 AC XY: 5241 AN XY: 22560

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.296

Gnomad4 SAS exome AF: 0.275

Gnomad4 FIN exome AF: 0.266

Gnomad4 NFE exome AF: 0.186

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.204 AC: 29201 AN: 143326 Hom.: 3016 Cov.: 0 AF XY: 0.209 AC XY: 14531 AN XY: 69624

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.219

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;