rs6833149

Variant names:

• chr4-27009920-T-A
• rs6833149
• NM_020860.4:c.1489+918T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-27009920-T-A
• chr4-27009920-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020860.4(STIM2):​c.1489+918T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,148 control chromosomes in the GnomAD database, including 7,757 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 0.32 (7757 hom., cov: 33)
• Consequence: STIM2 NM_020860.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STIM2	NM_020860.4	c.1489+918T>A		intron_variant	Intron 10 of 11	ENST00000467087.7	NP_065911.3
STIM2	NM_001169118.2	c.1513+918T>A		intron_variant	Intron 11 of 12		NP_001162589.1
STIM2	NM_001169117.2	c.1489+918T>A		intron_variant	Intron 10 of 12		NP_001162588.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STIM2	ENST00000467087.7	c.1489+918T>A		intron_variant	Intron 10 of 11	1	NM_020860.4	ENSP00000419073.2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48294 AN: 152030 Hom.: 7758 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.297

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.318 AC: 48329 AN: 152148 Hom.: 7757 Cov.: 33 AF XY: 0.320 AC XY: 23808 AN XY: 74370

African (AFR) AF: 0.337 AC: 13976 AN: 41484

American (AMR) AF: 0.344 AC: 5255 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2013 AN: 5170

South Asian (SAS) AF: 0.330 AC: 1589 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3138 AN: 10574

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20301 AN: 68014

Other (OTH) AF: 0.298 AC: 631 AN: 2114

Alfa AF: 0.306 Hom.: 919

Bravo AF: 0.317

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.080
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: rs6833149; hg19: chr4-27011542;