Genetic Variant MED13L:c.311-37101_311-37098delTATA (chr12-116148609-CTATA-C) – 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_311-37098delTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 182,350 control chromosomes in the GnomAD database, including 3,348 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3016 hom., cov: 0)

Exomes 𝑓: 0.23 ( 332 hom. )

Consequence

MED13L
NM_015335.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

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 (SAS) allele frequency at 95% confidence interval = 0.257 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_311-37098delTATA		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_311-37098delTATA		intron_variant	Intron 2 of 30	1	NM_015335.5	ENSP00000281928.3		Q71F56

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

29198

AN:

143308

Hom.:

3016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.218

GnomAD3 exomes

AF:

0.241

AC:

7602

AN:

31506

Hom.:

259

AF XY:

0.239

AC XY:

4136

AN XY:

17292

show subpopulations

Gnomad AFR exome

AF:

0.231

Gnomad AMR exome

AF:

0.199

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.317

Gnomad SAS exome

AF:

0.279

Gnomad FIN exome

AF:

0.281

Gnomad NFE exome

AF:

0.214

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.229

AC:

8944

AN:

39024

Hom.:

332

AF XY:

0.232

AC XY:

5241

AN XY:

22560

show subpopulations

Gnomad4 AFR exome

AF:

0.130

Gnomad4 AMR exome

AF:

0.180

Gnomad4 ASJ exome

AF:

0.134

Gnomad4 EAS exome

AF:

0.296

Gnomad4 SAS exome

AF:

0.275

Gnomad4 FIN exome

AF:

0.266

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.184

GnomAD4 genome

AF:

0.204

AC:

29201

AN:

143326

Hom.:

3016

Cov.:

AF XY:

0.209

AC XY:

14531

AN XY:

69624

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.270

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

12-116148609-CTATATATATA-CTATATA

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