7-144074785-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001386096.1(OR2A25):c.566C>T(p.Ala189Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,138 control chromosomes in the GnomAD database, including 1 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 (★).
Frequency
Consequence
NM_001386096.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2A25 | NM_001386096.1 | c.566C>T | p.Ala189Val | missense_variant | 2/2 | ENST00000641663.1 | |
OR2A25 | NM_001004488.2 | c.566C>T | p.Ala189Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2A25 | ENST00000641663.1 | c.566C>T | p.Ala189Val | missense_variant | 2/2 | NM_001386096.1 | P1 | ||
OR2A25 | ENST00000408898.2 | c.566C>T | p.Ala189Val | missense_variant | 1/1 | P1 | |||
OR2A25 | ENST00000641441.1 | c.566C>T | p.Ala189Val | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000680 AC: 17AN: 249892Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135550
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461856Hom.: 1 Cov.: 52 AF XY: 0.0000440 AC XY: 32AN XY: 727228
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | 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