rs5746096
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000636.4(SOD2):c.29G>T(p.Ser10Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000657 in 1,605,776 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000636.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOD2 | NM_000636.4 | c.29G>T | p.Ser10Ile | missense_variant | 2/5 | ENST00000538183.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOD2 | ENST00000538183.7 | c.29G>T | p.Ser10Ile | missense_variant | 2/5 | 1 | NM_000636.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00164 AC: 250AN: 152218Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000949 AC: 219AN: 230756Hom.: 0 AF XY: 0.000894 AC XY: 112AN XY: 125254
GnomAD4 exome AF: 0.000554 AC: 805AN: 1453440Hom.: 1 Cov.: 32 AF XY: 0.000556 AC XY: 402AN XY: 722686
GnomAD4 genome ? AF: 0.00164 AC: 250AN: 152336Hom.: 0 Cov.: 31 AF XY: 0.00176 AC XY: 131AN XY: 74504
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at