14-20034290-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004714.2(OR4K13):c.469T>A(p.Ser157Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,194 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_001004714.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR4K13 | NM_001004714.2 | c.469T>A | p.Ser157Thr | missense_variant | 2/2 | ENST00000641904.1 | NP_001004714.1 | |
OR4K13 | NM_001386029.1 | c.469T>A | p.Ser157Thr | missense_variant | 2/2 | NP_001372958.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR4K13 | ENST00000641904.1 | c.469T>A | p.Ser157Thr | missense_variant | 2/2 | NM_001004714.2 | ENSP00000492930.1 | |||
OR4K13 | ENST00000641664.1 | c.469T>A | p.Ser157Thr | missense_variant | 2/2 | ENSP00000493405.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 34
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.469T>A (p.S157T) alteration is located in exon 1 (coding exon 1) of the OR4K13 gene. This alteration results from a T to A substitution at nucleotide position 469, causing the serine (S) at amino acid position 157 to be replaced by a threonine (T). 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