chr2-71133151-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005791.3(MPHOSPH10):c.343C>T(p.Arg115Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,978 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R115H) has been classified as Likely benign.
Frequency
Consequence
NM_005791.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPHOSPH10 | NM_005791.3 | c.343C>T | p.Arg115Cys | missense_variant | 2/11 | ENST00000244230.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH10 | ENST00000244230.7 | c.343C>T | p.Arg115Cys | missense_variant | 2/11 | 1 | NM_005791.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251296Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135832
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461808Hom.: 1 Cov.: 36 AF XY: 0.0000454 AC XY: 33AN XY: 727190
GnomAD4 genome AF: 0.000302 AC: 46AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at