14-20117516-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004715.5(OR4K17):c.17A>T(p.Gln6Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000377 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004715.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR4K17 | NM_001004715.5 | c.17A>T | p.Gln6Leu | missense_variant | 2/2 | ENST00000641386.2 | NP_001004715.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR4K17 | ENST00000641386.2 | c.17A>T | p.Gln6Leu | missense_variant | 2/2 | NM_001004715.5 | ENSP00000493449.2 | |||
OR4K17 | ENST00000641633.2 | c.17A>T | p.Gln6Leu | missense_variant | 3/3 | ENSP00000493115.2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152080Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251282Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135794
GnomAD4 exome AF: 0.000397 AC: 580AN: 1461706Hom.: 0 Cov.: 32 AF XY: 0.000367 AC XY: 267AN XY: 727158
GnomAD4 genome AF: 0.000184 AC: 28AN: 152080Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.110A>T (p.Q37L) alteration is located in exon 1 (coding exon 1) of the OR4K17 gene. This alteration results from a A to T substitution at nucleotide position 110, causing the glutamine (Q) at amino acid position 37 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