rs7801498
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001126340.3(ORAI2):c.*2096G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,026 control chromosomes in the GnomAD database, including 24,281 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.55 ( 24272 hom., cov: 32)
Exomes 𝑓: 0.70 ( 9 hom. )
Consequence
ORAI2
NM_001126340.3 3_prime_UTR
NM_001126340.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.41
Genes affected
ORAI2 (HGNC:21667): (ORAI calcium release-activated calcium modulator 2) Predicted to enable store-operated calcium channel activity. Predicted to be involved in store-operated calcium entry. Predicted to be located in growth cone. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ORAI2 | NM_001126340.3 | c.*2096G>A | 3_prime_UTR_variant | 4/4 | ENST00000495936.7 | ||
ORAI2 | NM_001271818.2 | c.*2096G>A | 3_prime_UTR_variant | 4/4 | |||
ORAI2 | NM_001271819.2 | c.*2096G>A | 3_prime_UTR_variant | 3/3 | |||
ORAI2 | NM_032831.4 | c.*2096G>A | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ORAI2 | ENST00000495936.7 | c.*2096G>A | 3_prime_UTR_variant | 4/4 | 2 | NM_001126340.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.550 AC: 83484AN: 151876Hom.: 24280 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD4 exome AF: 0.700 AC: 21AN: 30Hom.: 9 Cov.: 0 AF XY: 0.773 AC XY: 17AN XY: 22
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GnomAD4 genome ? AF: 0.549 AC: 83493AN: 151996Hom.: 24272 Cov.: 32 AF XY: 0.543 AC XY: 40349AN XY: 74284
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at