19-8731603-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001004699.3(OR2Z1):c.575C>A(p.Thr192Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,386 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign 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. T192S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001004699.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2Z1 | NM_001004699.3 | c.575C>A | p.Thr192Asn | missense_variant | 3/3 | ENST00000641125.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2Z1 | ENST00000641125.1 | c.575C>A | p.Thr192Asn | missense_variant | 3/3 | NM_001004699.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000231 AC: 35AN: 151622Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251278Hom.: 1 AF XY: 0.000162 AC XY: 22AN XY: 135822
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461764Hom.: 1 Cov.: 33 AF XY: 0.0000578 AC XY: 42AN XY: 727200
GnomAD4 genome ? AF: 0.000231 AC: 35AN: 151622Hom.: 0 Cov.: 32 AF XY: 0.000270 AC XY: 20AN XY: 74096
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.575C>A (p.T192N) alteration is located in exon 1 (coding exon 1) of the OR2Z1 gene. This alteration results from a C to A substitution at nucleotide position 575, causing the threonine (T) at amino acid position 192 to be replaced by an asparagine (N). 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