chr11-123805439-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.911G>A(p.Arg304Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,459,924 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR6M1 | NM_001005325.1 | c.911G>A | p.Arg304Lys | missense_variant | 1/1 | ENST00000309154.3 | NP_001005325.1 | |
LOC105369544 | XR_948125.1 | n.506+7447C>T | intron_variant | |||||
LOC105369544 | XR_948126.1 | n.483+7447C>T | intron_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249260Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134650
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1459924Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726256
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.911G>A (p.R304K) 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 911, causing the arginine (R) at amino acid position 304 to be replaced by a lysine (K). 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