6-159907497-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002377.4(MAS1):c.542G>A(p.Arg181Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R181W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002377.4 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 |
---|---|---|---|---|---|---|---|
MAS1 | NM_002377.4 | c.542G>A | p.Arg181Gln | missense_variant | 3/3 | ENST00000674077.2 | |
MAS1 | NM_001366704.2 | c.542G>A | p.Arg181Gln | missense_variant | 2/2 | ||
MAS1 | XM_047418776.1 | c.542G>A | p.Arg181Gln | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAS1 | ENST00000674077.2 | c.542G>A | p.Arg181Gln | missense_variant | 3/3 | NM_002377.4 | P1 | ||
MAS1 | ENST00000252660.5 | c.542G>A | p.Arg181Gln | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152004Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250980Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135640
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461770Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727180
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152004Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74246
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at