chr16-69711242-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
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 0.207 in 1,610,182 control chromosomes in the GnomAD database, including 37,821 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000903.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NQO1 | NM_000903.3 | c.559C>T | p.Pro187Ser | missense_variant | Exon 6 of 6 | ENST00000320623.10 | NP_000894.1 | |
NQO1 | NM_001025433.2 | c.457C>T | p.Pro153Ser | missense_variant | Exon 5 of 5 | NP_001020604.1 | ||
NQO1 | NM_001025434.2 | c.445C>T | p.Pro149Ser | missense_variant | Exon 5 of 5 | NP_001020605.1 | ||
NQO1 | NM_001286137.2 | c.343C>T | p.Pro115Ser | missense_variant | Exon 4 of 4 | NP_001273066.1 |
Ensembl
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 Cov.: 33 AF XY: 0.208 AC XY: 150960AN XY: 724570
GnomAD4 genome AF: 0.217 AC: 32929AN: 152066Hom.: 3888 Cov.: 32 AF XY: 0.223 AC XY: 16554AN XY: 74316
ClinVar
Submissions by phenotype
RECLASSIFIED - NQO1 POLYMORPHISM Benign:1
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NQO1-related disorder Benign:1
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