17-3421492-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012373.3(OR3A3):c.907G>A(p.Ala303Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,549,474 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 Uncertain significance (★).
Frequency
Consequence
NM_012373.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR3A3 | NM_001386098.1 | c.907G>A | p.Ala303Thr | missense_variant | 2/2 | NP_001373027.1 | ||
OR3A3 | NM_012373.3 | c.907G>A | p.Ala303Thr | missense_variant | 3/3 | NP_036505.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR3A3 | ENST00000641141.1 | c.907G>A | p.Ala303Thr | missense_variant | 3/3 | ENSP00000493061.1 | ||||
OR3A3 | ENST00000574571.4 | c.907G>A | p.Ala303Thr | missense_variant | 1/1 | 6 | ENSP00000493211.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000349 AC: 7AN: 200692Hom.: 0 AF XY: 0.0000566 AC XY: 6AN XY: 106076
GnomAD4 exome AF: 0.0000458 AC: 64AN: 1397308Hom.: 0 Cov.: 34 AF XY: 0.0000524 AC XY: 36AN XY: 687334
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.925G>A (p.A309T) alteration is located in exon 1 (coding exon 1) of the OR3A3 gene. This alteration results from a G to A substitution at nucleotide position 925, causing the alanine (A) at amino acid position 309 to be replaced by a threonine (T). 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