11-55967629-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005491.2(OR10AG1):āc.895A>Gā(p.Ile299Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,459,432 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 (ā ).
Frequency
Consequence
NM_001005491.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR10AG1 | NM_001005491.2 | c.895A>G | p.Ile299Val | missense_variant | 2/2 | ENST00000641071.2 | NP_001005491.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR10AG1 | ENST00000641071.2 | c.895A>G | p.Ile299Val | missense_variant | 2/2 | NM_001005491.2 | ENSP00000493281.2 | |||
OR10AG1 | ENST00000312345.4 | c.835A>G | p.Ile279Val | missense_variant | 1/1 | 6 | ENSP00000311477.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250980Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135676
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459432Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726210
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.835A>G (p.I279V) alteration is located in exon 1 (coding exon 1) of the OR10AG1 gene. This alteration results from a A to G substitution at nucleotide position 835, causing the isoleucine (I) at amino acid position 279 to be replaced by a valine (V). 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