16-3204502-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370640.6(OR1F1):āc.256A>Gā(p.Ile86Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,613,966 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 (ā ).
Frequency
Consequence
NM_001370640.6 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 |
---|---|---|---|---|---|---|---|---|
OR1F1 | NM_001370640.6 | c.256A>G | p.Ile86Val | 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.256A>G | p.Ile86Val | missense_variant | 4/4 | NM_001370640.6 | ENSP00000305424 | P1 | ||
OR1F1 | ENST00000576468.1 | n.418+13165A>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
OR1F1 | ENST00000652759.1 | n.424-839A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251488Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135918
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461886Hom.: 0 Cov.: 46 AF XY: 0.0000619 AC XY: 45AN XY: 727244
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.256A>G (p.I86V) alteration is located in exon 1 (coding exon 1) of the OR1F1 gene. This alteration results from a A to G substitution at nucleotide position 256, causing the isoleucine (I) at amino acid position 86 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at