7-102439014-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001126340.3(ORAI2):c.58G>A(p.Gly20Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00021 in 1,613,846 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ORAI2 | NM_001126340.3 | c.58G>A | p.Gly20Ser | missense_variant | Exon 3 of 4 | ENST00000495936.7 | NP_001119812.1 | |
ORAI2 | NM_001271818.2 | c.58G>A | p.Gly20Ser | missense_variant | Exon 3 of 4 | NP_001258747.1 | ||
ORAI2 | NM_032831.4 | c.58G>A | p.Gly20Ser | missense_variant | Exon 2 of 3 | NP_116220.1 | ||
ORAI2 | NM_001271819.2 | c.-7+2681G>A | intron_variant | Intron 2 of 2 | NP_001258748.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000378 AC: 95AN: 251112Hom.: 1 AF XY: 0.000361 AC XY: 49AN XY: 135856
GnomAD4 exome AF: 0.000209 AC: 306AN: 1461758Hom.: 2 Cov.: 31 AF XY: 0.000224 AC XY: 163AN XY: 727184
GnomAD4 genome AF: 0.000217 AC: 33AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.58G>A (p.G20S) alteration is located in exon 3 (coding exon 1) of the ORAI2 gene. This alteration results from a G to A substitution at nucleotide position 58, causing the glycine (G) at amino acid position 20 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