chr19-8731776-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004699.3(OR2Z1):c.748C>A(p.Leu250Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,614,226 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001004699.3 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 |
---|---|---|---|---|---|---|---|
OR2Z1 | NM_001004699.3 | c.748C>A | p.Leu250Ile | missense_variant | 3/3 | ENST00000641125.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2Z1 | ENST00000641125.1 | c.748C>A | p.Leu250Ile | missense_variant | 3/3 | NM_001004699.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251460Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135894
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 727246
GnomAD4 genome AF: 0.000407 AC: 62AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.748C>A (p.L250I) 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 748, causing the leucine (L) at amino acid position 250 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