chr1-158547801-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001005189.2(OR6Y1):c.305G>T(p.Cys102Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,613,356 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C102Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005189.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR6Y1 | NM_001005189.2 | c.305G>T | p.Cys102Phe | missense_variant | 2/2 | ENST00000641622.1 | |
OR6Y1 | NM_001386050.1 | c.305G>T | p.Cys102Phe | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR6Y1 | ENST00000641622.1 | c.305G>T | p.Cys102Phe | missense_variant | 2/2 | NM_001005189.2 | P1 | ||
OR6Y1 | ENST00000641282.1 | c.305G>T | p.Cys102Phe | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000725 AC: 11AN: 151632Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250890Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135566
GnomAD4 exome AF: 0.000209 AC: 306AN: 1461724Hom.: 0 Cov.: 33 AF XY: 0.000179 AC XY: 130AN XY: 727170
GnomAD4 genome AF: 0.0000725 AC: 11AN: 151632Hom.: 0 Cov.: 32 AF XY: 0.0000540 AC XY: 4AN XY: 74090
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2024 | The c.305G>T (p.C102F) alteration is located in exon 1 (coding exon 1) of the OR6Y1 gene. This alteration results from a G to T substitution at nucleotide position 305, causing the cysteine (C) at amino acid position 102 to be replaced by a phenylalanine (F). 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