GeneBe

12-116148609-CTATATATATA-CTATATATATATATATATATATATA

Position:

Variant summary

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

The NM_015335.5(MED13L):​c.311-37111_311-37098dupTATATATATATATA 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 0.000063 ( 0 hom., cov: 0)

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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MED13LNM_015335.5 linkuse as main transcriptc.311-37111_311-37098dupTATATATATATATA intron_variant ENST00000281928.9 NP_056150.1 Q71F56

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MED13LENST00000281928.9 linkuse as main transcriptc.311-37111_311-37098dupTATATATATATATA intron_variant 1 NM_015335.5 ENSP00000281928.3 Q71F56

Frequencies

GnomAD3 genomes
AF:
0.0000627
AC:
9
AN:
143470
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000128
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000280
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
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
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.0000627
AC:
9
AN:
143470
Hom.:
0
Cov.:
0
AF XY:
0.0000717
AC XY:
5
AN XY:
69692
show subpopulations
Gnomad4 AFR
AF:
0.000128
Gnomad4 AMR
AF:
0.000280
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
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

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.

Other links and lift over

dbSNP: rs3043743; hg19: chr12-116586414; API