rs10263

Variant names:

• chr4-27023875-A-G
• rs10263
• NM_020860.4:c.*879A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-27023875-A-G
• chr4-27023875-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020860.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STIM2	NM_020860.4	MANE Select	c.*879A>G		3_prime_UTR	Exon 12 of 12	NP_065911.3
	STIM2	NM_001169118.2		c.*879A>G		3_prime_UTR	Exon 13 of 13	NP_001162589.1
	STIM2	NM_001169117.2		c.*1388A>G		3_prime_UTR	Exon 13 of 13	NP_001162588.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STIM2	ENST00000467087.7	TSL:1 MANE Select	c.*879A>G		3_prime_UTR	Exon 12 of 12	ENSP00000419073.2
	STIM2	ENST00000465503.6	TSL:1	c.*879A>G		3_prime_UTR	Exon 13 of 13	ENSP00000417569.2
	STIM2	ENST00000467011.6	TSL:1	c.*1388A>G		3_prime_UTR	Exon 13 of 13	ENSP00000419383.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0701 AC: 30 AN: 428

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.104 AC: 4326 AN: 41524

American (AMR) AF: 0.102 AC: 1558 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5168

South Asian (SAS) AF: 0.147 AC: 709 AN: 4828

European-Finnish (FIN) AF: 0.0814 AC: 864 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0814 AC: 5538 AN: 68002

Other (OTH) AF: 0.104 AC: 220 AN: 2116

Alfa AF: 0.0925 Hom.: 285

Bravo AF: 0.104

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10263; hg19: chr4-27025497;