11-3855883-CTCTCTTCTCT-CTCTCT

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001382567.1(STIM1):c.-370_-366delTCTTC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 237,122 control chromosomes in the GnomAD database, including 12,371 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7795 hom., cov: 0)

Exomes 𝑓: 0.32 ( 4576 hom. )

Consequence

STIM1
NM_001382567.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.755

Publications

4 publications found

Variant links:

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 links:

MIR4687 (HGNC:41712): (microRNA 4687) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR4687 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 11-3855883-CTCTCT-C is Benign according to our data. Variant chr11-3855883-CTCTCT-C is described in ClinVar as Benign. ClinVar VariationId is 1249545.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STIM1	NM_001382567.1	MANE Select	c.-370_-366delTCTTC	5_prime_UTR	Exon 1 of 13	NP_001369496.1	H0YDB2
STIM1	NM_001277961.3		c.-370_-366delTCTTC	5_prime_UTR	Exon 1 of 12	NP_001264890.1	G0XQ39
STIM1	NM_001382568.1		c.-370_-366delTCTTC	5_prime_UTR	Exon 1 of 12	NP_001369497.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STIM1	ENST00000526596.2	TSL:5 MANE Select	c.-370_-366delTCTTC	5_prime_UTR	Exon 1 of 13	ENSP00000433266.2	H0YDB2
STIM1	ENST00000616714.4	TSL:1	c.-370_-366delTCTTC	5_prime_UTR	Exon 1 of 12	ENSP00000478059.1	G0XQ39
STIM1	ENST00000300737.8	TSL:1	c.-370_-366delTCTTC	5_prime_UTR	Exon 1 of 12	ENSP00000300737.4	Q13586-1

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46144

AN:

151570

Hom.:

7792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.379

Gnomad EAS

AF:

0.352

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.324

GnomAD4 exome

AF:

0.319

AC:

27227

AN:

85434

Hom.:

4576

AF XY:

0.312

AC XY:

14603

AN XY:

46876

show subpopulations

African (AFR)

AF:

0.116

AC:

282

AN:

2438

American (AMR)

AF:

0.371

AC:

1717

AN:

4624

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

594

AN:

1810

East Asian (EAS)

AF:

0.336

AC:

1300

AN:

3874

South Asian (SAS)

AF:

0.253

AC:

4189

AN:

16578

European-Finnish (FIN)

AF:

0.319

AC:

1198

AN:

3760

Middle Eastern (MID)

AF:

0.286

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.342

AC:

16354

AN:

47770

Other (OTH)

AF:

0.352

AC:

1513

AN:

4300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

860

1720

2581

3441

4301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

150

300

450

600

750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.304

AC:

46178

AN:

151688

Hom.:

7795

Cov.:

AF XY:

0.303

AC XY:

22461

AN XY:

74122

show subpopulations

African (AFR)

AF:

0.140

AC:

5805

AN:

41500

American (AMR)

AF:

0.376

AC:

5741

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

1315

AN:

3466

East Asian (EAS)

AF:

0.352

AC:

1790

AN:

5080

South Asian (SAS)

AF:

0.282

AC:

1359

AN:

4816

European-Finnish (FIN)

AF:

0.370

AC:

3885

AN:

10500

Middle Eastern (MID)

AF:

0.390

AC:

114

AN:

292

European-Non Finnish (NFE)

AF:

0.372

AC:

25219

AN:

67768

Other (OTH)

AF:

0.323

AC:

681

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1538

3076

4615

6153

7691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.135

Hom.:

257

Bravo

AF:

0.302

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.76

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over