6-29174319-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_030905.3(OR2J2):āc.684C>Gā(p.Ser228Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_030905.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR2J2 | NM_030905.3 | c.684C>G | p.Ser228Arg | missense_variant | 2/2 | ENST00000641417.1 | NP_112167.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR2J2 | ENST00000641417.1 | c.684C>G | p.Ser228Arg | missense_variant | 2/2 | NM_030905.3 | ENSP00000493401 | P1 | ||
OR2J2 | ENST00000377167.3 | c.684C>G | p.Ser228Arg | missense_variant | 1/1 | ENSP00000366372 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152040Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249188Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135184
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461690Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 727136
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152040Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74266
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 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