12-116148609-CTATATATATA-CTATA

Position:

• chr12-116148609-CTATATATATA-CTATA

Variant summary

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

The NM_015335.5(MED13L):​c.311-37103_311-37098delTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 182,132 control chromosomes in the GnomAD database, including 171 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.035 (134 hom., cov: 0)
  • Exomes 𝑓: 0.044 (37 hom.)
• Consequence: MED13L NM_015335.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

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 = 0.0538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MED13L	NM_015335.5	c.311-37103_311-37098delTATATA		intron_variant		ENST00000281928.9	NP_056150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MED13L	ENST00000281928.9	c.311-37103_311-37098delTATATA		intron_variant		1	NM_015335.5	ENSP00000281928.3

Frequencies

GnomAD3 genomes AF: 0.0350 AC: 5016 AN: 143410 Hom.: 128 Cov.: 0

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0102

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00741

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0882

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0434

GnomAD3 exomes AF: 0.0452 AC: 1423 AN: 31506 Hom.: 37 AF XY: 0.0475 AC XY: 821 AN XY: 17292

Gnomad AFR exome AF: 0.0716

Gnomad AMR exome AF: 0.0267

Gnomad ASJ exome AF: 0.115

Gnomad EAS exome AF: 0.0149

Gnomad SAS exome AF: 0.0591

Gnomad FIN exome AF: 0.0217

Gnomad NFE exome AF: 0.0492

Gnomad OTH exome AF: 0.0520

GnomAD4 exome AF: 0.0444 AC: 1717 AN: 38704 Hom.: 37 AF XY: 0.0492 AC XY: 1103 AN XY: 22398

Gnomad4 AFR exome AF: 0.0435

Gnomad4 AMR exome AF: 0.0370

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.0433

Gnomad4 SAS exome AF: 0.0731

Gnomad4 FIN exome AF: 0.0202

Gnomad4 NFE exome AF: 0.0506

Gnomad4 OTH exome AF: 0.0582

GnomAD4 genome AF: 0.0351 AC: 5033 AN: 143428 Hom.: 134 Cov.: 0 AF XY: 0.0350 AC XY: 2439 AN XY: 69704

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.0276

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.00744

Gnomad4 SAS AF: 0.0596

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.0432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;