7-102446822-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001126340.3(ORAI2):c.535C>T(p.Arg179Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001126340.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ORAI2 | NM_001126340.3 | c.535C>T | p.Arg179Trp | missense_variant | Exon 4 of 4 | ENST00000495936.7 | NP_001119812.1 | |
ORAI2 | NM_001271818.2 | c.535C>T | p.Arg179Trp | missense_variant | Exon 4 of 4 | NP_001258747.1 | ||
ORAI2 | NM_032831.4 | c.535C>T | p.Arg179Trp | missense_variant | Exon 3 of 3 | NP_116220.1 | ||
ORAI2 | NM_001271819.2 | c.304C>T | p.Arg102Trp | missense_variant | Exon 3 of 3 | NP_001258748.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250852Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135670
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461588Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727112
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.535C>T (p.R179W) alteration is located in exon 4 (coding exon 2) of the ORAI2 gene. This alteration results from a C to T substitution at nucleotide position 535, causing the arginine (R) at amino acid position 179 to be replaced by a tryptophan (W). 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