chr4-24799693-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003102.4(SOD3):c.172G>A(p.Ala58Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 1,578,062 control chromosomes in the GnomAD database, including 302,909 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003102.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOD3 | NM_003102.4 | c.172G>A | p.Ala58Thr | missense_variant | 2/2 | ENST00000382120.4 | |
SOD3 | XR_427488.2 | n.267G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOD3 | ENST00000382120.4 | c.172G>A | p.Ala58Thr | missense_variant | 2/2 | 1 | NM_003102.4 | P1 | |
SOD3 | ENST00000598411.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.502 AC: 76267AN: 151936Hom.: 22372 Cov.: 33
GnomAD3 exomes AF: 0.552 AC: 100699AN: 182560Hom.: 29607 AF XY: 0.565 AC XY: 57280AN XY: 101358
GnomAD4 exome AF: 0.618 AC: 881954AN: 1426010Hom.: 280545 Cov.: 69 AF XY: 0.617 AC XY: 436815AN XY: 707466
GnomAD4 genome AF: 0.502 AC: 76261AN: 152052Hom.: 22364 Cov.: 33 AF XY: 0.504 AC XY: 37452AN XY: 74332
ClinVar
Submissions by phenotype
SOD3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at