rs2073151
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013936.4(OR12D2):c.475G>A(p.Val159Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,612,186 control chromosomes in the GnomAD database, including 139,700 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 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 same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V159A) has been classified as Uncertain significance.
Frequency
Consequence
NM_013936.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR12D2 | NM_013936.4 | c.475G>A | p.Val159Ile | missense_variant | 2/2 | ENST00000642051.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR12D2 | ENST00000642051.1 | c.475G>A | p.Val159Ile | missense_variant | 2/2 | NM_013936.4 | P1 | ||
OR12D2 | ENST00000623183.1 | c.475G>A | p.Val159Ile | missense_variant | 1/1 | P1 | |||
OR5V1 | ENST00000377154.1 | c.-83+25433C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes AF: 0.359 AC: 54426AN: 151720Hom.: 10548 Cov.: 31
GnomAD3 exomes AF: 0.391 AC: 96189AN: 246240Hom.: 19671 AF XY: 0.389 AC XY: 52125AN XY: 134158
GnomAD4 exome AF: 0.416 AC: 607337AN: 1460348Hom.: 129145 Cov.: 45 AF XY: 0.414 AC XY: 300627AN XY: 726484
GnomAD4 genome AF: 0.359 AC: 54438AN: 151838Hom.: 10555 Cov.: 31 AF XY: 0.359 AC XY: 26634AN XY: 74186
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at