11-123806271-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005325.1(OR6M1):c.79G>A(p.Val27Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,882 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 (★).
Frequency
Consequence
NM_001005325.1 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 | UniProt |
---|---|---|---|---|---|---|---|
OR6M1 | NM_001005325.1 | c.79G>A | p.Val27Met | missense_variant | 1/1 | ENST00000309154.3 | |
LOC105369544 | XR_948125.1 | n.506+8279C>T | intron_variant, non_coding_transcript_variant | ||||
LOC105369544 | XR_948126.1 | n.483+8279C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR6M1 | ENST00000309154.3 | c.79G>A | p.Val27Met | missense_variant | 1/1 | NM_001005325.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250508Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135350
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461718Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727154
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.79G>A (p.V27M) alteration is located in exon 1 (coding exon 1) of the OR6M1 gene. This alteration results from a G to A substitution at nucleotide position 79, causing the valine (V) at amino acid position 27 to be replaced by a methionine (M). 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