X-131544558-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001004486.1(OR13H1):c.485C>A(p.Ser162Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,208,651 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004486.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR13H1 | NM_001004486.1 | c.485C>A | p.Ser162Tyr | missense_variant | 1/1 | ENST00000338616.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13H1 | ENST00000338616.6 | c.485C>A | p.Ser162Tyr | missense_variant | 1/1 | NM_001004486.1 | P1 | ||
IGSF1 | ENST00000370904.6 | c.-913+34110G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000898 AC: 1AN: 111412Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33582
GnomAD3 exomes AF: 0.0000656 AC: 12AN: 182927Hom.: 0 AF XY: 0.0000741 AC XY: 5AN XY: 67515
GnomAD4 exome AF: 0.0000301 AC: 33AN: 1097239Hom.: 0 Cov.: 34 AF XY: 0.0000496 AC XY: 18AN XY: 362607
GnomAD4 genome AF: 0.00000898 AC: 1AN: 111412Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33582
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 01, 2023 | The c.485C>A (p.S162Y) alteration is located in exon 1 (coding exon 1) of the OR13H1 gene. This alteration results from a C to A substitution at nucleotide position 485, causing the serine (S) at amino acid position 162 to be replaced by a tyrosine (Y). 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