chr4-27023875-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020860.4(STIM2):​c.*879A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).

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>T		3_prime_UTR	Exon 12 of 12	NP_065911.3
	STIM2	NM_001169118.2		c.*879A>T		3_prime_UTR	Exon 13 of 13	NP_001162589.1	H0Y860
	STIM2	NM_001169117.2		c.*1388A>T		3_prime_UTR	Exon 13 of 13	NP_001162588.1	Q9P246-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STIM2	ENST00000467087.7	TSL:1 MANE Select	c.*879A>T		3_prime_UTR	Exon 12 of 12	ENSP00000419073.2	Q9P246-1
	STIM2	ENST00000465503.6	TSL:1	c.*879A>T		3_prime_UTR	Exon 13 of 13	ENSP00000417569.2	H0Y860
	STIM2	ENST00000467011.6	TSL:1	c.*1388A>T		3_prime_UTR	Exon 13 of 13	ENSP00000419383.2	Q9P246-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.72

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;