chr1-158420047-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004476.2(OR10K2):āc.820A>Cā(p.Ile274Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,613,580 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_001004476.2 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 |
---|---|---|---|---|---|---|---|
OR10K2 | NM_001004476.2 | c.820A>C | p.Ile274Leu | missense_variant | 2/2 | ENST00000641042.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR10K2 | ENST00000641042.1 | c.820A>C | p.Ile274Leu | missense_variant | 2/2 | NM_001004476.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 37AN: 250666Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135438
GnomAD4 exome AF: 0.0000883 AC: 129AN: 1461492Hom.: 0 Cov.: 33 AF XY: 0.0000922 AC XY: 67AN XY: 727064
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | The c.820A>C (p.I274L) alteration is located in exon 1 (coding exon 1) of the OR10K2 gene. This alteration results from a A to C substitution at nucleotide position 820, causing the isoleucine (I) at amino acid position 274 to be replaced by a leucine (L). 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