Genetic Variant ORAI2:p.Ser67Ser (chr7-102439157-C-T) – ACMG Classification: Benign (-21 pts)

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -5.44

Variant links:

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]

ORAI2 links:

Genome browser will be placed here

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 link	c.201C>T	p.Ser67Ser	synonymous_variant	Exon 3 of 4	ENST00000495936.7	NP_001119812.1	Q96SN7
ORAI2	NM_001271818.2 link	c.201C>T	p.Ser67Ser	synonymous_variant	Exon 3 of 4		NP_001258747.1	Q96SN7
ORAI2	NM_032831.4 link	c.201C>T	p.Ser67Ser	synonymous_variant	Exon 2 of 3		NP_116220.1	Q96SN7
ORAI2	NM_001271819.2 link	c.-7+2824C>T		intron_variant	Intron 2 of 2		NP_001258748.1	B4DUB4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ORAI2	ENST00000495936.7 link	c.201C>T	p.Ser67Ser	synonymous_variant	Exon 3 of 4	2	NM_001126340.3	ENSP00000420178.2		Q96SN7C9JQR7

Frequencies

GnomAD3 genomes

AF:

0.0154

AC:

2340

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0510

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00720

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000999

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.00453

AC:

1131

AN:

249902

Hom.:

AF XY:

0.00336

AC XY:

455

AN XY:

135510

show subpopulations

Gnomad AFR exome

AF:

0.0515

Gnomad AMR exome

AF:

0.00362

Gnomad ASJ exome

AF:

0.000299

Gnomad EAS exome

AF:

0.0000545

Gnomad SAS exome

AF:

0.000457

Gnomad FIN exome

AF:

0.000787

Gnomad NFE exome

AF:

0.00111

Gnomad OTH exome

AF:

0.00393

GnomAD4 exome

AF:

0.00234

AC:

3426

AN:

1461402

Hom.:

Cov.:

AF XY:

0.00212

AC XY:

1540

AN XY:

727026

show subpopulations

Gnomad4 AFR exome

AF:

0.0546

Gnomad4 AMR exome

AF:

0.00402

Gnomad4 ASJ exome

AF:

0.000268

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000278

Gnomad4 FIN exome

AF:

0.000566

Gnomad4 NFE exome

AF:

0.000916

Gnomad4 OTH exome

AF:

0.00474

GnomAD4 genome

AF:

0.0154

AC:

2345

AN:

152324

Hom.:

Cov.:

AF XY:

0.0148

AC XY:

1102

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0510

Gnomad4 AMR

AF:

0.00719

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00100

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.00790

Hom.:

Bravo

AF:

0.0177

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.00136

EpiControl

AF:

0.00172

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.15

DANN

Benign

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over