16-3204478-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001370640.6(OR1F1):c.232G>A(p.Val78Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,842 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 Likely benign (★).
Frequency
Consequence
NM_001370640.6 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1F1 | NM_001370640.6 | c.232G>A | p.Val78Ile | missense_variant | 4/4 | ENST00000304646.3 | NP_001357569.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR1F1 | ENST00000304646.3 | c.232G>A | p.Val78Ile | missense_variant | 4/4 | NM_001370640.6 | ENSP00000305424 | P1 | ||
OR1F1 | ENST00000576468.1 | n.418+13141G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
OR1F1 | ENST00000652759.1 | n.424-863G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251478Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135910
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461864Hom.: 0 Cov.: 45 AF XY: 0.0000165 AC XY: 12AN XY: 727236
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151978Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74224
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 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