chr20-50960127-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014484.5(MOCS3):āc.1285T>Gā(p.Ser429Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,614,230 control chromosomes in the GnomAD database, including 125 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S429L) has been classified as Uncertain significance.
Frequency
Consequence
NM_014484.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MOCS3 | NM_014484.5 | c.1285T>G | p.Ser429Ala | missense_variant | 1/1 | ENST00000244051.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MOCS3 | ENST00000244051.3 | c.1285T>G | p.Ser429Ala | missense_variant | 1/1 | NM_014484.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00655 AC: 997AN: 152222Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00630 AC: 1584AN: 251436Hom.: 7 AF XY: 0.00678 AC XY: 922AN XY: 135906
GnomAD4 exome AF: 0.0107 AC: 15599AN: 1461890Hom.: 121 Cov.: 32 AF XY: 0.0106 AC XY: 7676AN XY: 727244
GnomAD4 genome AF: 0.00654 AC: 996AN: 152340Hom.: 4 Cov.: 33 AF XY: 0.00595 AC XY: 443AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at