1-158547627-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001005189.2(OR6Y1):c.479C>T(p.Thr160Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,613,320 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005189.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR6Y1 | NM_001005189.2 | c.479C>T | p.Thr160Ile | missense_variant | 2/2 | ENST00000641622.1 | NP_001005189.1 | |
OR6Y1 | NM_001386050.1 | c.479C>T | p.Thr160Ile | missense_variant | 2/2 | NP_001372979.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR6Y1 | ENST00000641622.1 | c.479C>T | p.Thr160Ile | missense_variant | 2/2 | NM_001005189.2 | ENSP00000492894 | P1 | ||
OR6Y1 | ENST00000641282.1 | c.479C>T | p.Thr160Ile | missense_variant | 2/2 | ENSP00000493253 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000152 AC: 23AN: 151658Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000327 AC: 82AN: 250648Hom.: 0 AF XY: 0.000384 AC XY: 52AN XY: 135494
GnomAD4 exome AF: 0.000225 AC: 329AN: 1461548Hom.: 2 Cov.: 33 AF XY: 0.000257 AC XY: 187AN XY: 727048
GnomAD4 genome AF: 0.000152 AC: 23AN: 151772Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.479C>T (p.T160I) alteration is located in exon 1 (coding exon 1) of the OR6Y1 gene. This alteration results from a C to T substitution at nucleotide position 479, causing the threonine (T) at amino acid position 160 to be replaced by an isoleucine (I). 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