chr14-19935838-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001004063.3(OR4K1):c.172C>T(p.Pro58Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004063.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR4K1 | NM_001004063.3 | c.172C>T | p.Pro58Ser | missense_variant | Exon 2 of 2 | ENST00000641172.1 | NP_001004063.2 | |
OR4K1 | XM_011537153.3 | c.172C>T | p.Pro58Ser | missense_variant | Exon 3 of 3 | XP_011535455.1 | ||
LOC124903278 | XR_007064055.1 | n.165+7887G>A | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR4K1 | ENST00000641172.1 | c.172C>T | p.Pro58Ser | missense_variant | Exon 2 of 2 | NM_001004063.3 | ENSP00000493193.1 | |||
OR4K1 | ENST00000285600.4 | c.172C>T | p.Pro58Ser | missense_variant | Exon 1 of 1 | 6 | ENSP00000285600.3 | |||
OR4K1 | ENST00000641429.1 | c.172C>T | p.Pro58Ser | missense_variant | Exon 3 of 3 | ENSP00000493205.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 37
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251318Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135832
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461872Hom.: 0 Cov.: 58 AF XY: 0.00000275 AC XY: 2AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 37 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.172C>T (p.P58S) alteration is located in exon 1 (coding exon 1) of the OR4K1 gene. This alteration results from a C to T substitution at nucleotide position 172, causing the proline (P) at amino acid position 58 to be replaced by a serine (S). 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