rs9284879
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001145030.2(TOPAZ1):c.586G>A(p.Val196Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 1,546,734 control chromosomes in the GnomAD database, including 197,564 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_001145030.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TOPAZ1 | NM_001145030.2 | c.586G>A | p.Val196Ile | missense_variant | Exon 2 of 20 | ENST00000309765.4 | NP_001138502.1 | |
TOPAZ1 | XM_011533694.3 | c.586G>A | p.Val196Ile | missense_variant | Exon 2 of 20 | XP_011531996.1 | ||
TOPAZ1 | XM_017006361.2 | c.586G>A | p.Val196Ile | missense_variant | Exon 2 of 18 | XP_016861850.1 | ||
TOPAZ1 | XM_017006362.1 | c.586G>A | p.Val196Ile | missense_variant | Exon 2 of 15 | XP_016861851.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.461 AC: 70098AN: 151910Hom.: 17403 Cov.: 33
GnomAD3 exomes AF: 0.554 AC: 85047AN: 153438Hom.: 24660 AF XY: 0.561 AC XY: 45556AN XY: 81216
GnomAD4 exome AF: 0.501 AC: 699148AN: 1394706Hom.: 180150 Cov.: 39 AF XY: 0.507 AC XY: 348269AN XY: 687196
GnomAD4 genome AF: 0.461 AC: 70141AN: 152028Hom.: 17414 Cov.: 33 AF XY: 0.471 AC XY: 35025AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at