rs1133472
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001126340.3(ORAI2):c.201C>T(p.Ser67Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00358 in 1,613,726 control chromosomes in the GnomAD database, including 115 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.015 ( 54 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 61 hom. )
Consequence
ORAI2
NM_001126340.3 synonymous
NM_001126340.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.44
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 7-102439157-C-T is Benign according to our data. Variant chr7-102439157-C-T is described in ClinVar as [Benign]. Clinvar id is 783502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-5.44 with no splicing effect.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ORAI2 | NM_001126340.3 | c.201C>T | p.Ser67Ser | synonymous_variant | Exon 3 of 4 | ENST00000495936.7 | NP_001119812.1 | |
ORAI2 | NM_001271818.2 | c.201C>T | p.Ser67Ser | synonymous_variant | Exon 3 of 4 | NP_001258747.1 | ||
ORAI2 | NM_032831.4 | c.201C>T | p.Ser67Ser | synonymous_variant | Exon 2 of 3 | NP_116220.1 | ||
ORAI2 | NM_001271819.2 | c.-7+2824C>T | intron_variant | Intron 2 of 2 | NP_001258748.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2340AN: 152206Hom.: 54 Cov.: 32
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GnomAD3 exomes AF: 0.00453 AC: 1131AN: 249902Hom.: 24 AF XY: 0.00336 AC XY: 455AN XY: 135510
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GnomAD4 exome AF: 0.00234 AC: 3426AN: 1461402Hom.: 61 Cov.: 31 AF XY: 0.00212 AC XY: 1540AN XY: 727026
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GnomAD4 genome AF: 0.0154 AC: 2345AN: 152324Hom.: 54 Cov.: 32 AF XY: 0.0148 AC XY: 1102AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Aug 02, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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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