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GeneBe

rs4968469

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_005121.3(MED13):c.301+3343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,968 control chromosomes in the GnomAD database, including 13,452 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 13452 hom., cov: 32)

Consequence

MED13
NM_005121.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34
Variant links:
Genes affected
MED13 (HGNC:22474): (mediator complex subunit 13) This gene encodes a component of the mediator complex (also known as TRAP, SMCC, DRIP, or ARC), a transcriptional coactivator complex thought to be required for the expression of almost all genes. The mediator complex is recruited by transcriptional activators or nuclear receptors to induce gene expression, possibly by interacting with RNA polymerase II and promoting the formation of a transcriptional pre-initiation complex. The product of this gene is proposed to form a sub-complex with MED12, cyclin C, and CDK8 that can negatively regulate transactivation by mediator. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MED13NM_005121.3 linkuse as main transcriptc.301+3343A>G intron_variant ENST00000397786.7
MED13XM_011525551.3 linkuse as main transcriptc.301+3343A>G intron_variant
MED13XM_011525552.3 linkuse as main transcriptc.301+3343A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MED13ENST00000397786.7 linkuse as main transcriptc.301+3343A>G intron_variant 1 NM_005121.3 P1

Frequencies

GnomAD3 genomes
AF:
0.378
AC:
57414
AN:
151850
Hom.:
13402
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.624
Gnomad AMI
AF:
0.225
Gnomad AMR
AF:
0.289
Gnomad ASJ
AF:
0.275
Gnomad EAS
AF:
0.725
Gnomad SAS
AF:
0.465
Gnomad FIN
AF:
0.367
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.227
Gnomad OTH
AF:
0.336
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.379
AC:
57525
AN:
151968
Hom.:
13452
Cov.:
32
AF XY:
0.386
AC XY:
28680
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.625
Gnomad4 AMR
AF:
0.289
Gnomad4 ASJ
AF:
0.275
Gnomad4 EAS
AF:
0.725
Gnomad4 SAS
AF:
0.465
Gnomad4 FIN
AF:
0.367
Gnomad4 NFE
AF:
0.226
Gnomad4 OTH
AF:
0.343
Alfa
AF:
0.249
Hom.:
5674
Bravo
AF:
0.384
Asia WGS
AF:
0.573
AC:
1991
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.30
Cadd
Benign
22
Dann
Benign
0.78

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.

Other links and lift over

dbSNP: rs4968469; hg19: chr17-60137085; API