9-122800619-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_080859.1(OR1K1):c.497G>A(p.Arg166His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,612,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080859.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR1K1 | NM_080859.1 | c.497G>A | p.Arg166His | missense_variant | 1/1 | ENST00000277309.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR1K1 | ENST00000277309.3 | c.497G>A | p.Arg166His | missense_variant | 1/1 | NM_080859.1 | P1 | ||
PDCL | ENST00000436632.5 | c.254-2080C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000808 AC: 20AN: 247582Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134394
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460202Hom.: 0 Cov.: 33 AF XY: 0.0000619 AC XY: 45AN XY: 726480
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at