11-55368004-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001005275.2(OR4A15):c.31A>T(p.Ile11Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 1,613,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005275.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR4A15 | NM_001005275.2 | c.31A>T | p.Ile11Phe | missense_variant | 1/1 | ENST00000641526.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR4A15 | ENST00000641526.1 | c.31A>T | p.Ile11Phe | missense_variant | 1/1 | NM_001005275.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250458Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135364
GnomAD4 exome AF: 0.000128 AC: 187AN: 1461288Hom.: 0 Cov.: 33 AF XY: 0.000122 AC XY: 89AN XY: 726948
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.121A>T (p.I41F) alteration is located in exon 1 (coding exon 1) of the OR4A15 gene. This alteration results from a A to T substitution at nucleotide position 121, causing the isoleucine (I) at amino acid position 41 to be replaced by a phenylalanine (F). 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