dbSNP rs7210080: SSTR2:c.*534T>C (chr17-73170963-T-C) – 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.*534T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 348,256 control chromosomes in the GnomAD database, including 16,931 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 0.33 ( 9236 hom., cov: 32)

Exomes 𝑓: 0.27 ( 7695 hom. )

Consequence

SSTR2
NM_001050.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.693

Publications

15 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR2	NM_001050.3 link	c.*534T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000357585.4	NP_001041.1	P30874-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR2	ENST00000357585.4 link	c.*534T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_001050.3	ENSP00000350198.2		P30874-1
ENSG00000264860	ENST00000580671.1 link	n.312+5675T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49500

AN:

152004

Hom.:

9217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.364

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.315

GnomAD4 exome

AF:

0.272

AC:

53348

AN:

196134

Hom.:

7695

Cov.:

AF XY:

0.279

AC XY:

29700

AN XY:

106594

show subpopulations

African (AFR)

AF:

0.524

AC:

2685

AN:

5122

American (AMR)

AF:

0.383

AC:

3918

AN:

10234

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

1052

AN:

4112

East Asian (EAS)

AF:

0.298

AC:

2431

AN:

8164

South Asian (SAS)

AF:

0.351

AC:

12312

AN:

35124

European-Finnish (FIN)

AF:

0.161

AC:

3572

AN:

22158

Middle Eastern (MID)

AF:

0.302

AC:

184

AN:

610

European-Non Finnish (NFE)

AF:

0.244

AC:

24836

AN:

101712

Other (OTH)

AF:

0.265

AC:

2358

AN:

8898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1779

3558

5338

7117

8896

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.326

AC:

49553

AN:

152122

Hom.:

9236

Cov.:

AF XY:

0.322

AC XY:

23935

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.508

AC:

21078

AN:

41482

American (AMR)

AF:

0.365

AC:

5576

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

835

AN:

3470

East Asian (EAS)

AF:

0.312

AC:

1611

AN:

5166

South Asian (SAS)

AF:

0.336

AC:

1619

AN:

4820

European-Finnish (FIN)

AF:

0.155

AC:

1642

AN:

10590

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.237

AC:

16084

AN:

68000

Other (OTH)

AF:

0.313

AC:

662

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1610

3220

4830

6440

8050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.272

Hom.:

11922

Bravo

AF:

0.350

Asia WGS

AF:

0.331

AC:

1149

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

(source)

DANN

Benign

0.57

PhyloP100

-0.69

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