Genetic Variant MED13L:c.311-37101_311-37098dupTATA (chr12-116148609-C-CTATA) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.54

Variant links:

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]

MED13L links:

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]

MIR620 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
MED13L	NM_015335.5 link	c.311-37101_311-37098dupTATA		intron_variant	Intron 2 of 30	ENST00000281928.9	NP_056150.1	Q71F56

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MED13L	ENST00000281928.9 link	c.311-37101_311-37098dupTATA		intron_variant	Intron 2 of 30	1	NM_015335.5	ENSP00000281928.3		Q71F56

Frequencies

GnomAD3 genomes

AF:

0.0248

AC:

3551

AN:

143410

Hom.:

120

Cov.:

show subpopulations

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.:

AF XY:

0.00324

AC XY:

AN XY:

17292

show subpopulations

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:

AN:

39778

Hom.:

Cov.:

AF XY:

0.00213

AC XY:

AN XY:

22968

show subpopulations

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.:

AF XY:

0.0235

AC XY:

1637

AN XY:

69698

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over