1-248294849-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004692.2(OR2T12):c.730G>T(p.Ala244Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,612,868 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_001004692.2 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 |
---|---|---|---|---|---|---|---|
OR2T12 | NM_001004692.2 | c.730G>T | p.Ala244Ser | missense_variant | 3/3 | ENST00000641276.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2T12 | ENST00000641276.1 | c.730G>T | p.Ala244Ser | missense_variant | 3/3 | NM_001004692.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152110Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251122Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135714
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460640Hom.: 0 Cov.: 102 AF XY: 0.0000234 AC XY: 17AN XY: 726658
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152228Hom.: 0 Cov.: 29 AF XY: 0.0000269 AC XY: 2AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.730G>T (p.A244S) alteration is located in exon 1 (coding exon 1) of the OR2T12 gene. This alteration results from a G to T substitution at nucleotide position 730, causing the alanine (A) at amino acid position 244 to be replaced by a serine (S). 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