Variant rs6822297 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000467087.7(STIM2):c.625+26A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,417,130 control chromosomes in the GnomAD database, including 142,886 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 0.37 ( 11538 hom., cov: 31)

Exomes 𝑓: 0.45 ( 131348 hom. )

Consequence

STIM2
ENST00000467087.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.132

Variant links:

Genes affected

STIM2 (HGNC:19205): (stromal interaction molecule 2) This gene is a member of the stromal interaction molecule (STIM) family and likely arose, along with related family member STIM1, from a common ancestral gene. The encoded protein functions to regulate calcium concentrations in the cytosol and endoplasmic reticulum, and is involved in the activation of plasma membrane Orai Ca(2+) entry channels. This gene initiates translation from a non-AUG (UUG) start site. A signal peptide is cleaved from the resulting protein. Multiple transcript variants result from alternative splicing. [provided by RefSeq, Dec 2009]

STIM2 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
STIM2	NM_020860.4 linkuse as main transcript	c.625+26A>G	intron_variant	ENST00000467087.7	NP_065911.3
STIM2	NM_001169117.2 linkuse as main transcript	c.625+26A>G	intron_variant		NP_001162588.1
STIM2	NM_001169118.2 linkuse as main transcript	c.625+26A>G	intron_variant		NP_001162589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STIM2	ENST00000467087.7 linkuse as main transcript	c.625+26A>G		intron_variant		1	NM_020860.4	ENSP00000419073	P2	Q9P246-1

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55736

AN:

151790

Hom.:

11535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.534

Gnomad AMR

AF:

0.364

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.338

Gnomad NFE

AF:

0.470

Gnomad OTH

AF:

0.391

GnomAD3 exomes

AF:

0.418

AC:

91503

AN:

218690

Hom.:

20141

AF XY:

0.425

AC XY:

50567

AN XY:

119088

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.400

Gnomad ASJ exome

AF:

0.455

Gnomad EAS exome

AF:

0.178

Gnomad SAS exome

AF:

0.397

Gnomad FIN exome

AF:

0.489

Gnomad NFE exome

AF:

0.479

Gnomad OTH exome

AF:

0.438

GnomAD4 exome

AF:

0.448

AC:

566783

AN:

1265222

Hom.:

131348

Cov.:

AF XY:

0.447

AC XY:

284490

AN XY:

637106

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.453

Gnomad4 EAS exome

AF:

0.148

Gnomad4 SAS exome

AF:

0.391

Gnomad4 FIN exome

AF:

0.489

Gnomad4 NFE exome

AF:

0.473

Gnomad4 OTH exome

AF:

0.422

GnomAD4 genome

AF:

0.367

AC:

55754

AN:

151908

Hom.:

11538

Cov.:

AF XY:

0.367

AC XY:

27273

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.364

Gnomad4 ASJ

AF:

0.442

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.470

Gnomad4 OTH

AF:

0.386

Alfa

AF:

0.446

Hom.:

27015

Bravo

AF:

0.352

Asia WGS

AF:

0.265

AC:

923

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.36

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over