12-116148609-CTATATATATA-CTA

Position:

• chr12-116148609-CTATATATATA-CTA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_015335.5(MED13L):​c.311-37105_311-37098delTATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000316 in 183,258 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000091 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0011 (0 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MED13L	NM_015335.5	c.311-37105_311-37098delTATATATA		intron_variant		ENST00000281928.9	NP_056150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MED13L	ENST00000281928.9	c.311-37105_311-37098delTATATATA		intron_variant		1	NM_015335.5	ENSP00000281928.3

Frequencies

GnomAD3 genomes AF: 0.0000906 AC: 13 AN: 143468 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000231

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000700

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000601

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000603 AC: 19 AN: 31506 Hom.: 0 AF XY: 0.000636 AC XY: 11 AN XY: 17292

Gnomad AFR exome AF: 0.00302

Gnomad AMR exome AF: 0.000990

Gnomad ASJ exome AF: 0.00171

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000962

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000623

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00113 AC: 45 AN: 39774 Hom.: 0 AF XY: 0.00118 AC XY: 27 AN XY: 22960

Gnomad4 AFR exome AF: 0.0109

Gnomad4 AMR exome AF: 0.00122

Gnomad4 ASJ exome AF: 0.00277

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00315

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00115

Gnomad4 OTH exome AF: 0.00300

GnomAD4 genome AF: 0.0000906 AC: 13 AN: 143484 Hom.: 0 Cov.: 0 AF XY: 0.0000860 AC XY: 6 AN XY: 69728

Gnomad4 AFR AF: 0.000230

Gnomad4 AMR AF: 0.0000700

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000603

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;