NM_005121.3:c.6117+349G>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005121.3(MED13):c.6117+349G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,144 control chromosomes in the GnomAD database, including 1,997 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 0.16 ( 1997 hom., cov: 32)
Consequence
MED13
NM_005121.3 intron
NM_005121.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.780
Publications
4 publications found
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]
MED13 Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- intellectual developmental disorder 61Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Illumina, Labcorp Genetics (formerly Invitae), G2P
- syndromic intellectual disabilityInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED13 | NM_005121.3 | c.6117+349G>C | intron_variant | Intron 27 of 29 | ENST00000397786.7 | NP_005112.2 | ||
MED13 | XM_011525551.3 | c.5958+349G>C | intron_variant | Intron 26 of 28 | XP_011523853.1 | |||
MED13 | XM_011525553.4 | c.5448+349G>C | intron_variant | Intron 24 of 26 | XP_011523855.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.156 AC: 23778AN: 152026Hom.: 1999 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
23778
AN:
152026
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.156 AC: 23779AN: 152144Hom.: 1997 Cov.: 32 AF XY: 0.151 AC XY: 11226AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
23779
AN:
152144
Hom.:
Cov.:
32
AF XY:
AC XY:
11226
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
7354
AN:
41484
American (AMR)
AF:
AC:
2466
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
716
AN:
3468
East Asian (EAS)
AF:
AC:
334
AN:
5180
South Asian (SAS)
AF:
AC:
385
AN:
4818
European-Finnish (FIN)
AF:
AC:
960
AN:
10582
Middle Eastern (MID)
AF:
AC:
93
AN:
294
European-Non Finnish (NFE)
AF:
AC:
10954
AN:
68004
Other (OTH)
AF:
AC:
404
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1056
2112
3167
4223
5279
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
246
492
738
984
1230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
308
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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