3-98469841-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001004736.4(OR5K1):āc.265A>Gā(p.Asn89Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000505 in 1,613,318 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N89S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001004736.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR5K1 | NM_001004736.4 | c.265A>G | p.Asn89Asp | missense_variant | 2/2 | ENST00000642057.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR5K1 | ENST00000642057.1 | c.265A>G | p.Asn89Asp | missense_variant | 2/2 | NM_001004736.4 | P1 | ||
OR5K1 | ENST00000332650.5 | c.265A>G | p.Asn89Asp | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00304 AC: 462AN: 152030Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251238Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135800
GnomAD4 exome AF: 0.000237 AC: 346AN: 1461168Hom.: 3 Cov.: 31 AF XY: 0.000208 AC XY: 151AN XY: 726946
GnomAD4 genome AF: 0.00308 AC: 468AN: 152150Hom.: 1 Cov.: 32 AF XY: 0.00268 AC XY: 199AN XY: 74378
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at