Genetic Variant MED13L:c.311-37099_311-37098delTA (chr12-116148609-CTA-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.311-37099_311-37098delTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 180,914 control chromosomes in the GnomAD database, including 7,381 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 7256 hom., cov: 0)

Exomes 𝑓: 0.25 ( 125 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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MED13L	NM_015335.5 link	c.311-37099_311-37098delTA		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.311-37099_311-37098delTA		intron_variant	Intron 2 of 30	1	NM_015335.5	ENSP00000281928.3		Q71F56

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

44887

AN:

143214

Hom.:

7259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.511

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.271

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.285

GnomAD3 exomes

AF:

0.299

AC:

9420

AN:

31506

Hom.:

119

AF XY:

0.306

AC XY:

5296

AN XY:

17292

show subpopulations

Gnomad AFR exome

AF:

0.303

Gnomad AMR exome

AF:

0.374

Gnomad ASJ exome

AF:

0.284

Gnomad EAS exome

AF:

0.401

Gnomad SAS exome

AF:

0.387

Gnomad FIN exome

AF:

0.258

Gnomad NFE exome

AF:

0.291

Gnomad OTH exome

AF:

0.279

GnomAD4 exome

AF:

0.252

AC:

9514

AN:

37682

Hom.:

125

AF XY:

0.258

AC XY:

5625

AN XY:

21834

show subpopulations

Gnomad4 AFR exome

AF:

0.348

Gnomad4 AMR exome

AF:

0.289

Gnomad4 ASJ exome

AF:

0.254

Gnomad4 EAS exome

AF:

0.281

Gnomad4 SAS exome

AF:

0.343

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.262

GnomAD4 genome

AF:

0.313

AC:

44893

AN:

143232

Hom.:

7256

Cov.:

AF XY:

0.318

AC XY:

22100

AN XY:

69598

show subpopulations

Gnomad4 AFR

AF:

0.400

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.249

Gnomad4 EAS

AF:

0.510

Gnomad4 SAS

AF:

0.450

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.285

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-CTATATATA

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