6-29374545-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030959.3(OR12D3):c.743G>A(p.Cys248Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030959.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR12D3 | NM_030959.3 | c.743G>A | p.Cys248Tyr | missense_variant | 1/1 | ENST00000396806.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR12D3 | ENST00000396806.3 | c.743G>A | p.Cys248Tyr | missense_variant | 1/1 | NM_030959.3 | P1 | ||
OR5V1 | ENST00000377154.1 | c.-82-18268G>A | intron_variant | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000325 AC: 8AN: 246358Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134266
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460756Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726692
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2023 | The c.743G>A (p.C248Y) alteration is located in exon 1 (coding exon 1) of the OR12D3 gene. This alteration results from a G to A substitution at nucleotide position 743, causing the cysteine (C) at amino acid position 248 to be replaced by a tyrosine (Y). 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