rs3043743

Variant names:

• chr12-116148609-CTATATATATA-C
• rs3043743
• NM_015335.5:c.311-37107_311-37098delTATATATATA

Your query was ambiguous. Multiple possible variants found:

• chr12-116148609-CTATATATATA-C
• chr12-116148609-CTATATATATA-CTA
• chr12-116148609-CTATATATATA-CTATA
• chr12-116148609-CTATATATATA-CTATATA
• chr12-116148609-CTATATATATA-CTATATATA
• chr12-116148609-CTATATATATA-CTATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATATATATATATATA
• chr12-116148609-CTATATATATA-CTATATATATATATATATATATATATATATATA

Variant summary

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

The NM_015335.5(MED13L):​c.311-37107_311-37098delTATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 183,326 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 0.00010 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00033 (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:32876): (microRNA 620) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MED13L	NM_015335.5	c.311-37107_311-37098delTATATATATA		intron_variant	Intron 2 of 30	ENST00000281928.9	NP_056150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MED13L	ENST00000281928.9	c.311-37107_311-37098delTATATATATA		intron_variant	Intron 2 of 30	1	NM_015335.5	ENSP00000281928.3

Frequencies

GnomAD3 genomes AF: 0.000105 AC: 15 AN: 143470 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00173

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000917

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000326 AC: 13 AN: 39838 Hom.: 0 AF XY: 0.000348 AC XY: 8 AN XY: 22994

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00182

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000153

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000105 AC: 15 AN: 143488 Hom.: 0 Cov.: 0 AF XY: 0.0000860 AC XY: 6 AN XY: 69730

Gnomad4 AFR AF: 0.0000256

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00174

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000917

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;