chr16-3204988-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370640.6(OR1F1):c.742G>C(p.Val248Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370640.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR1F1 | NM_001370640.6 | c.742G>C | p.Val248Leu | missense_variant | 4/4 | ENST00000304646.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR1F1 | ENST00000304646.3 | c.742G>C | p.Val248Leu | missense_variant | 4/4 | NM_001370640.6 | P1 | ||
OR1F1 | ENST00000576468.1 | n.418+13651G>C | intron_variant, non_coding_transcript_variant | 3 | |||||
OR1F1 | ENST00000652759.1 | n.424-353G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 27AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251464Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135902
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461886Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 727244
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.742G>C (p.V248L) alteration is located in exon 1 (coding exon 1) of the OR1F1 gene. This alteration results from a G to C substitution at nucleotide position 742, causing the valine (V) at amino acid position 248 to be replaced by a leucine (L). 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