dbSNP rs7220818: SSTR2:c.*133A>G (chr17-73170562-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001050.3(SSTR2):c.*133A>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 0.265 in 1,144,846 control chromosomes in the GnomAD database, including 43,242 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 0.29 ( 7092 hom., cov: 31)

Exomes 𝑓: 0.26 ( 36150 hom. )

Consequence

SSTR2
NM_001050.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.275

Publications

9 publications found

Variant links:

Genes affected

SSTR2 (HGNC:11331): (somatostatin receptor 2) Somatostatin acts at many sites to inhibit the release of many hormones and other secretory proteins. The biologic effects of somatostatin are probably mediated by a family of G protein-coupled receptors that are expressed in a tissue-specific manner. SSTR2 is a member of the superfamily of receptors having seven transmembrane segments and is expressed in highest levels in cerebrum and kidney. [provided by RefSeq, Jul 2008]

SSTR2 links:

ENSG00000264860 (HGNC:):

ENSG00000264860 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR2	NM_001050.3 link	c.*133A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000357585.4	NP_001041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR2	ENST00000357585.4 link	c.*133A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_001050.3	ENSP00000350198.2
ENSG00000264860	ENST00000580671.1 link	n.312+5274A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44726

AN:

151702

Hom.:

7077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.260

AC:

258171

AN:

993026

Hom.:

36150

Cov.:

AF XY:

0.262

AC XY:

133269

AN XY:

508198

show subpopulations

African (AFR)

AF:

0.390

AC:

9149

AN:

23448

American (AMR)

AF:

0.444

AC:

15639

AN:

35230

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

5812

AN:

22084

East Asian (EAS)

AF:

0.348

AC:

12018

AN:

34502

South Asian (SAS)

AF:

0.364

AC:

25633

AN:

70462

European-Finnish (FIN)

AF:

0.162

AC:

7892

AN:

48838

Middle Eastern (MID)

AF:

0.346

AC:

1699

AN:

4906

European-Non Finnish (NFE)

AF:

0.237

AC:

168065

AN:

708768

Other (OTH)

AF:

0.274

AC:

12264

AN:

44788

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

9939

19878

29816

39755

49694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4868

9736

14604

19472

24340

<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:

0.295

AC:

44776

AN:

151820

Hom.:

7092

Cov.:

AF XY:

0.293

AC XY:

21764

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.379

AC:

15668

AN:

41350

American (AMR)

AF:

0.381

AC:

5812

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

926

AN:

3472

East Asian (EAS)

AF:

0.313

AC:

1608

AN:

5138

South Asian (SAS)

AF:

0.353

AC:

1694

AN:

4796

European-Finnish (FIN)

AF:

0.156

AC:

1646

AN:

10554

Middle Eastern (MID)

AF:

0.408

AC:

119

AN:

292

European-Non Finnish (NFE)

AF:

0.240

AC:

16320

AN:

67954

Other (OTH)

AF:

0.304

AC:

643

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1557

3114

4671

6228

7785

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<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:

0.283

Hom.:

2815

Bravo

AF:

0.317

Asia WGS

AF:

0.349

AC:

1211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

6.1

(source)

DANN

Benign

0.84

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over