rs10263

chr4-27023875-A-Gchr4-27023875-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020860.4(STIM2):c.*879A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,668 control chromosomes in the GnomAD database, including 971 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 0.10 (971 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: STIM2 NM_020860.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STIM2	NM_020860.4	c.*879A>G		3_prime_UTR_variant	12/12	ENST00000467087.7
STIM2	NM_001169117.2	c.*1388A>G		3_prime_UTR_variant	13/13
STIM2	NM_001169118.2	c.*879A>G		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STIM2	ENST00000467087.7	c.*879A>G		3_prime_UTR_variant	12/12	1	NM_020860.4	P2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15467 AN: 152112 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0814

Gnomad OTH AF: 0.104

GnomAD4 exome AF: 0.0708 AC: 31 AN: 438 Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 19 AN XY: 266

Gnomad4 FIN exome AF: 0.0701

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.102 AC: 15460 AN: 152230 Hom.: 971 Cov.: 32 AF XY: 0.106 AC XY: 7873 AN XY: 74440

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0814

Gnomad4 NFE AF: 0.0814

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0926 Hom.: 222

Bravo AF: 0.104

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	13
Dann	Benign	0.71

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

Other links and lift over

dbSNP: rs10263; hg19: chr4-27025497;