1-248626730-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001001964.2(OR2T11):c.399G>A(p.Met133Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,573,106 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M133K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001001964.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000133 AC: 19AN: 142522Hom.: 3 Cov.: 28
GnomAD3 exomes AF: 0.000123 AC: 30AN: 244540Hom.: 3 AF XY: 0.0000982 AC XY: 13AN XY: 132382
GnomAD4 exome AF: 0.000150 AC: 215AN: 1430584Hom.: 21 Cov.: 38 AF XY: 0.000136 AC XY: 97AN XY: 711876
GnomAD4 genome AF: 0.000133 AC: 19AN: 142522Hom.: 3 Cov.: 28 AF XY: 0.000158 AC XY: 11AN XY: 69408
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.399G>A (p.M133I) alteration is located in exon 1 (coding exon 1) of the OR2T11 gene. This alteration results from a G to A substitution at nucleotide position 399, causing the methionine (M) at amino acid position 133 to be replaced by an isoleucine (I). 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