chr1-155610262-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_018116.4(MSTO1):c.14C>T(p.Ala5Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00157 in 764,272 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018116.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTO1 | NM_018116.4 | c.14C>T | p.Ala5Val | missense_variant | 1/14 | ENST00000245564.8 | |
LOC105371452 | XR_922171.2 | n.77-370G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.14C>T | p.Ala5Val | missense_variant | 1/14 | 1 | NM_018116.4 | P1 | |
ENST00000456382.2 | n.103+16G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00151 AC: 228AN: 151170Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.00134 AC: 154AN: 114550Hom.: 0 AF XY: 0.00131 AC XY: 80AN XY: 61184
GnomAD4 exome AF: 0.00159 AC: 974AN: 612988Hom.: 2 Cov.: 8 AF XY: 0.00158 AC XY: 503AN XY: 317660
GnomAD4 genome ? AF: 0.00151 AC: 228AN: 151284Hom.: 0 Cov.: 28 AF XY: 0.00135 AC XY: 100AN XY: 73878
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | MSTO1: PP2, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at