17-3215886-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014565.3(OR1A1):c.266G>A(p.Ser89Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,870 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_014565.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1A1 | NM_014565.3 | c.266G>A | p.Ser89Asn | missense_variant | 4/4 | ENST00000641732.2 | NP_055380.2 | |
OR1A1 | NM_001386104.1 | c.266G>A | p.Ser89Asn | missense_variant | 2/2 | NP_001373033.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251378Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135854
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461870Hom.: 0 Cov.: 68 AF XY: 0.0000110 AC XY: 8AN XY: 727232
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.266G>A (p.S89N) alteration is located in exon 1 (coding exon 1) of the OR1A1 gene. This alteration results from a G to A substitution at nucleotide position 266, causing the serine (S) at amino acid position 89 to be replaced by an asparagine (N). 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