9-122800351-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080859.1(OR1K1):c.229G>A(p.Val77Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080859.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR1K1 | NM_080859.1 | c.229G>A | p.Val77Ile | missense_variant | 1/1 | ENST00000277309.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR1K1 | ENST00000277309.3 | c.229G>A | p.Val77Ile | missense_variant | 1/1 | NM_080859.1 | P1 | ||
PDCL | ENST00000436632.5 | c.254-1812C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251434Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135886
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461870Hom.: 0 Cov.: 33 AF XY: 0.0000578 AC XY: 42AN XY: 727238
GnomAD4 genome AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.229G>A (p.V77I) alteration is located in exon 1 (coding exon 1) of the OR1K1 gene. This alteration results from a G to A substitution at nucleotide position 229, causing the valine (V) at amino acid position 77 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at