chr1-158717662-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001005327.3(OR6K3):c.454G>A(p.Gly152Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005327.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR6K3 | NM_001005327.3 | c.454G>A | p.Gly152Ser | missense_variant | 2/2 | ENST00000368145.2 | |
OR6K3 | XM_047420296.1 | c.454G>A | p.Gly152Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR6K3 | ENST00000368145.2 | c.454G>A | p.Gly152Ser | missense_variant | 2/2 | NM_001005327.3 | P1 | ||
OR6K3 | ENST00000368146.1 | c.502G>A | p.Gly168Ser | missense_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151906Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250628Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135398
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461620Hom.: 0 Cov.: 33 AF XY: 0.0000495 AC XY: 36AN XY: 727116
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151906Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 5AN XY: 74156
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.454G>A (p.G152S) alteration is located in exon 1 (coding exon 1) of the OR6K3 gene. This alteration results from a G to A substitution at nucleotide position 454, causing the glycine (G) at amino acid position 152 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