3-98087902-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_054106.1(OR5AC2):c.730G>A(p.Gly244Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,616 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 (no stars).
Frequency
Consequence
NM_054106.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR5AC2 | NM_054106.1 | c.730G>A | p.Gly244Ser | missense_variant | 1/1 | ENST00000358642.2 | NP_473447.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR5AC2 | ENST00000358642.2 | c.730G>A | p.Gly244Ser | missense_variant | 1/1 | NM_054106.1 | ENSP00000351466 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250640Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135534
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461572Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727030
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at