rs1800566
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1
The NM_000903.3(NQO1):c.559C>T(p.Pro187Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151948 control chromosomes in the gnomAD Genomes database, including 3881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic,risk factor (no stars). Synonymous variant affecting the same amino acid position (i.e. P187P) has been classified as Likely benign.
Frequency
Consequence
NM_000903.3 missense
Scores
Clinical Significance
Conservation
Links
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NQO1 | NM_000903.3 | c.559C>T | p.Pro187Ser | missense_variant | 6/6 | ENST00000320623.10 | |
NQO1 | NM_001025433.2 | c.457C>T | p.Pro153Ser | missense_variant | 5/5 | ||
NQO1 | NM_001025434.2 | c.445C>T | p.Pro149Ser | missense_variant | 5/5 | ||
NQO1 | NM_001286137.2 | c.343C>T | p.Pro115Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NQO1 | ENST00000320623.10 | c.559C>T | p.Pro187Ser | missense_variant | 6/6 | 1 | NM_000903.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.216 AC: 32896AN: 151948Hom.: 3881 Cov.: 32
GnomAD3 exomes AF: 0.252 AC: 62641AN: 248524Hom.: 9185 AF XY: 0.249 AC XY: 33426AN XY: 134474
GnomAD4 exome AF: 0.206 AC: 300203AN: 1458116Hom.: 33933 AF XY: 0.208 AC XY: 150960AN XY: 724570
ClinVar
Submissions by phenotype
Breast cancer, post-chemotherapy poor survival in Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2008 | - - |
Lung carcinoma Other:1
not provided, no assertion provided | literature only | Database of Curated Mutations (DoCM) | Mar 10, 2016 | - - |
Leukemia, post-chemotherapy, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2008 | - - |
Benzene toxicity, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at