6-29397174-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013936.4(OR12D2):c.475G>C(p.Val159Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 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 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR12D2 | NM_013936.4 | c.475G>C | p.Val159Leu | missense_variant | 2/2 | ENST00000642051.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR12D2 | ENST00000642051.1 | c.475G>C | p.Val159Leu | missense_variant | 2/2 | NM_013936.4 | P1 | ||
OR12D2 | ENST00000623183.1 | c.475G>C | p.Val159Leu | missense_variant | 1/1 | P1 | |||
OR5V1 | ENST00000377154.1 | c.-83+25433C>G | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151816Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246240Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134158
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000137 AC: 2AN: 1460740Hom.: 0 Cov.: 45 AF XY: 0.00000138 AC XY: 1AN XY: 726694
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151816Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74110
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at