12-116148609-CTATATATATA-CTATATATATATATA

Position:

• chr12-116148609-CTATATATATA-CTATATATATATATA

Variant summary

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

The NM_015335.5(MED13L):​c.311-37101_311-37098dupTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.025 (120 hom., cov: 0)
  • Exomes 𝑓: 0.0020 (0 hom.)
• Consequence: MED13L NM_015335.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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 (AFR) allele frequency at 95% confidence interval = 0.0742 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0248 AC: 3551 AN: 143410 Hom.: 120 Cov.: 0

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.000892

Gnomad EAS AF: 0.00160

Gnomad SAS AF: 0.00282

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00980

Gnomad NFE AF: 0.00428

Gnomad OTH AF: 0.0194

GnomAD3 exomes AF: 0.00375 AC: 118 AN: 31506 Hom.: 1 AF XY: 0.00324 AC XY: 56 AN XY: 17292

Gnomad AFR exome AF: 0.0313

Gnomad AMR exome AF: 0.00495

Gnomad ASJ exome AF: 0.00456

Gnomad EAS exome AF: 0.00136

Gnomad SAS exome AF: 0.00240

Gnomad FIN exome AF: 0.00170

Gnomad NFE exome AF: 0.00327

Gnomad OTH exome AF: 0.00839

GnomAD4 exome AF: 0.00204 AC: 81 AN: 39778 Hom.: 0 Cov.: 0 AF XY: 0.00213 AC XY: 49 AN XY: 22968

Gnomad4 AFR exome AF: 0.0326

Gnomad4 AMR exome AF: 0.00244

Gnomad4 ASJ exome AF: 0.00334

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00215

Gnomad4 FIN exome AF: 0.00145

Gnomad4 NFE exome AF: 0.00222

Gnomad4 OTH exome AF: 0.00301

GnomAD4 genome AF: 0.0248 AC: 3552 AN: 143426 Hom.: 120 Cov.: 0 AF XY: 0.0235 AC XY: 1637 AN XY: 69698

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0147

Gnomad4 ASJ AF: 0.000892

Gnomad4 EAS AF: 0.00161

Gnomad4 SAS AF: 0.00283

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00428

Gnomad4 OTH AF: 0.0193

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;