rs201987892
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP2BP4_ModerateBP6
The NM_015335.5(MED13L):c.3517G>A(p.Gly1173Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000193 in 1,614,040 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1173V) has been classified as Uncertain significance.
Frequency
Consequence
NM_015335.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED13L | NM_015335.5 | c.3517G>A | p.Gly1173Ser | missense_variant | 17/31 | ENST00000281928.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED13L | ENST00000281928.9 | c.3517G>A | p.Gly1173Ser | missense_variant | 17/31 | 1 | NM_015335.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152048Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 250956Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135622
GnomAD4 exome AF: 0.000197 AC: 288AN: 1461874Hom.: 2 Cov.: 32 AF XY: 0.000206 AC XY: 150AN XY: 727242
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74380
ClinVar
Submissions by phenotype
Transposition of the great arteries, dextro-looped;C4225208:Cardiac anomalies - developmental delay - facial dysmorphism syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
MED13L-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 16, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Transposition of the great arteries, dextro-looped Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at