chr11-56290474-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005199.2(OR8H1):c.589A>T(p.Met197Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,212 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_001005199.2 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 |
---|---|---|---|---|---|---|---|
OR8H1 | NM_001005199.2 | c.589A>T | p.Met197Leu | missense_variant | 2/2 | ENST00000641600.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR8H1 | ENST00000641600.1 | c.589A>T | p.Met197Leu | missense_variant | 2/2 | NM_001005199.2 | P1 | ||
OR8H1 | ENST00000313022.2 | c.589A>T | p.Met197Leu | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251322Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135816
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461866Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727238
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2024 | The c.589A>T (p.M197L) alteration is located in exon 1 (coding exon 1) of the OR8H1 gene. This alteration results from a A to T substitution at nucleotide position 589, causing the methionine (M) at amino acid position 197 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