20-50958850-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014484.5(MOCS3):āc.8C>Gā(p.Ser3Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000693 in 1,587,660 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 (ā ).
Frequency
Consequence
NM_014484.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MOCS3 | NM_014484.5 | c.8C>G | p.Ser3Cys | missense_variant | 1/1 | ENST00000244051.3 | NP_055299.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MOCS3 | ENST00000244051.3 | c.8C>G | p.Ser3Cys | missense_variant | 1/1 | NM_014484.5 | ENSP00000244051 | P1 | ||
DPM1 | ENST00000683466.1 | c.-264G>C | 5_prime_UTR_variant | 1/8 | ENSP00000507404 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239756Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130920
GnomAD4 exome AF: 0.00000488 AC: 7AN: 1435372Hom.: 0 Cov.: 32 AF XY: 0.00000423 AC XY: 3AN XY: 709442
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74442
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 18, 2023 | ClinVar contains an entry for this variant (Variation ID: 2076146). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with MOCS3-related conditions. This variant is present in population databases (rs187280062, gnomAD 0.009%). This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 3 of the MOCS3 protein (p.Ser3Cys). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at