chr11-58118841-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005211.2(OR9I1):c.604T>C(p.Phe202Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005211.2 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 |
---|---|---|---|---|---|---|---|
OR9I1 | NM_001005211.2 | c.604T>C | p.Phe202Leu | missense_variant | 3/3 | ENST00000641439.1 | |
OR9Q1 | NM_001005212.4 | c.-14-60590A>G | intron_variant | ENST00000335397.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR9I1 | ENST00000641439.1 | c.604T>C | p.Phe202Leu | missense_variant | 3/3 | NM_001005211.2 | P1 | ||
OR9Q1 | ENST00000335397.3 | c.-14-60590A>G | intron_variant | NM_001005212.4 | P1 | ||||
OR9I1 | ENST00000641478.1 | c.604T>C | p.Phe202Leu | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000599 AC: 15AN: 250318Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135256
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461684Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727142
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152372Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.604T>C (p.F202L) alteration is located in exon 1 (coding exon 1) of the OR9I1 gene. This alteration results from a T to C substitution at nucleotide position 604, causing the phenylalanine (F) at amino acid position 202 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