21-31659767-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_000454.5(SOD1):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_000454.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOD1 | ENST00000270142 | c.-3G>A | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_000454.5 | ENSP00000270142.7 | |||
SOD1 | ENST00000389995 | c.-3G>A | 5_prime_UTR_variant | Exon 1 of 5 | 3 | ENSP00000374645.4 | ||||
SOD1 | ENST00000470944.1 | n.59G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 2 | |||||
SOD1 | ENST00000476106.5 | n.75G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152282Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250426Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135688
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461532Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 727106
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74400
ClinVar
Submissions by phenotype
SOD1-related disorder Benign:1
This variant is classified as likely 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