16-3204622-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001370640.6(OR1F1):c.376G>A(p.Val126Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00554 in 1,614,032 control chromosomes in the GnomAD database, including 387 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001370640.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1F1 | NM_001370640.6 | c.376G>A | p.Val126Met | 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.376G>A | p.Val126Met | missense_variant | 4/4 | NM_001370640.6 | ENSP00000305424 | P1 | ||
OR1F1 | ENST00000576468.1 | n.418+13285G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
OR1F1 | ENST00000652759.1 | n.424-719G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0274 AC: 4165AN: 152040Hom.: 190 Cov.: 31
GnomAD3 exomes AF: 0.00733 AC: 1844AN: 251486Hom.: 73 AF XY: 0.00522 AC XY: 710AN XY: 135916
GnomAD4 exome AF: 0.00325 AC: 4757AN: 1461874Hom.: 196 Cov.: 49 AF XY: 0.00285 AC XY: 2072AN XY: 727238
GnomAD4 genome AF: 0.0275 AC: 4178AN: 152158Hom.: 191 Cov.: 31 AF XY: 0.0262 AC XY: 1953AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 04, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at