6-159907496-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002377.4(MAS1):c.541C>T(p.Arg181Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. R181Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002377.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAS1 | NM_002377.4 | c.541C>T | p.Arg181Trp | missense_variant | 3/3 | ENST00000674077.2 | |
MAS1 | NM_001366704.2 | c.541C>T | p.Arg181Trp | missense_variant | 2/2 | ||
MAS1 | XM_047418776.1 | c.541C>T | p.Arg181Trp | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAS1 | ENST00000674077.2 | c.541C>T | p.Arg181Trp | missense_variant | 3/3 | NM_002377.4 | P1 | ||
MAS1 | ENST00000252660.5 | c.541C>T | p.Arg181Trp | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 250970Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135646
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461774Hom.: 0 Cov.: 30 AF XY: 0.0000619 AC XY: 45AN XY: 727194
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.541C>T (p.R181W) alteration is located in exon 1 (coding exon 1) of the MAS1 gene. This alteration results from a C to T substitution at nucleotide position 541, causing the arginine (R) at amino acid position 181 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at