11-55913880-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001960.1(OR5W2):c.703T>A(p.Phe235Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,550 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_001001960.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151904Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250794Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135582
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461646Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727142
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151904Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.703T>A (p.F235I) alteration is located in exon 1 (coding exon 1) of the OR5W2 gene. This alteration results from a T to A substitution at nucleotide position 703, causing the phenylalanine (F) at amino acid position 235 to be replaced by an isoleucine (I). 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