chr11-5544700-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005289.5(OR52H1):āc.806A>Gā(p.Asn269Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N269H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005289.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR52H1 | NM_001005289.5 | c.806A>G | p.Asn269Ser | missense_variant | 2/2 | ENST00000322653.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR52H1 | ENST00000322653.7 | c.806A>G | p.Asn269Ser | missense_variant | 2/2 | NM_001005289.5 | P1 | ||
OR52H1 | ENST00000641796.2 | c.806A>G | p.Asn269Ser | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251436Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135890
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727246
GnomAD4 genome AF: 0.000309 AC: 47AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.824A>G (p.N275S) alteration is located in exon 1 (coding exon 1) of the OR52H1 gene. This alteration results from a A to G substitution at nucleotide position 824, causing the asparagine (N) at amino acid position 275 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