rs11828037

Variant names:

• chr11-3855664-A-G
• rs11828037
• NM_001382567.1:c.-607A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-3855664-A-G
• chr11-3855664-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001382567.1(STIM1):​c.-607A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 144,910 control chromosomes in the GnomAD database, including 16,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.48 (16166 hom., cov: 33)
  • Exomes 𝑓: 0.51 (20 hom.)
• Consequence: STIM1 NM_001382567.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0370
• Publications: 2 publications found

Genes affected

STIM1 (HGNC:11386): (stromal interaction molecule 1) This gene encodes a type 1 transmembrane protein that mediates Ca2+ influx after depletion of intracellular Ca2+ stores by gating of store-operated Ca2+ influx channels (SOCs). It is one of several genes located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocrotical carcinoma, and lung, ovarian, and breast cancer. This gene may play a role in malignancies and disease that involve this region, as well as early hematopoiesis, by mediating attachment to stromal cells. Mutations in this gene are associated with fatal classic Kaposi sarcoma, immunodeficiency due to defects in store-operated calcium entry (SOCE) in fibroblasts, ectodermal dysplasia and tubular aggregate myopathy. This gene is oriented in a head-to-tail configuration with the ribonucleotide reductase 1 gene (RRM1), with the 3' end of this gene situated 1.6 kb from the 5' end of the RRM1 gene. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]

STIM1-AS1 (HGNC:40568): (STIM1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 11-3855664-A-G is Benign according to our data. Variant chr11-3855664-A-G is described in ClinVar as Benign. ClinVar VariationId is 1289827.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382567.1. 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
	STIM1	NM_001382567.1	MANE Select	c.-607A>G		5_prime_UTR	Exon 1 of 13	NP_001369496.1	H0YDB2
	STIM1	NM_001382568.1		c.-607A>G		5_prime_UTR	Exon 1 of 12	NP_001369497.1
	STIM1	NM_003156.4		c.-607A>G		5_prime_UTR	Exon 1 of 12	NP_003147.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STIM1	ENST00000526596.2	TSL:5 MANE Select	c.-607A>G		5_prime_UTR	Exon 1 of 13	ENSP00000433266.2	H0YDB2
	STIM1	ENST00000952119.1		c.-607A>G		5_prime_UTR	Exon 1 of 13	ENSP00000622178.1
	STIM1	ENST00000862622.1		c.-607A>G		5_prime_UTR	Exon 1 of 12	ENSP00000532681.1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 68749 AN: 144728 Hom.: 16162 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.508 AC: 66 AN: 130 Hom.: 20 Cov.: 0 AF XY: 0.500 AC XY: 37 AN XY: 74

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.487 AC: 39 AN: 80

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.542 AC: 26 AN: 48

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.475 AC: 68771 AN: 144780 Hom.: 16166 Cov.: 33 AF XY: 0.479 AC XY: 33753 AN XY: 70458

African (AFR) AF: 0.455 AC: 18358 AN: 40324

American (AMR) AF: 0.475 AC: 6982 AN: 14692

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1247 AN: 3372

East Asian (EAS) AF: 0.550 AC: 2549 AN: 4634

South Asian (SAS) AF: 0.558 AC: 2544 AN: 4558

European-Finnish (FIN) AF: 0.498 AC: 4138 AN: 8308

Middle Eastern (MID) AF: 0.423 AC: 115 AN: 272

European-Non Finnish (NFE) AF: 0.480 AC: 31514 AN: 65700

Other (OTH) AF: 0.437 AC: 890 AN: 2036

Alfa AF: 0.474 Hom.: 2062

Bravo AF: 0.471

Asia WGS AF: 0.515 AC: 1744 AN: 3388

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.50
PhyloP100		0.037
PromoterAI		-0.067	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11828037; hg19: chr11-3876894;