chr6-41907076-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004275.5(MED20):c.635G>A(p.Arg212His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004275.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED20 | ENST00000265350.9 | c.635G>A | p.Arg212His | missense_variant | Exon 4 of 4 | 1 | NM_004275.5 | ENSP00000265350.4 | ||
ENSG00000288721 | ENST00000684631.1 | n.635G>A | non_coding_transcript_exon_variant | Exon 4 of 10 | ENSP00000507261.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151998Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251174Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135748
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461060Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726838
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151998Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74216
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 212 of the MED20 protein (p.Arg212His). This variant is present in population databases (rs140272550, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with MED20-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at