Genetic Variant SSTR2:c.-92-75A>G (chr17-73169153-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.-92-75A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 759,488 control chromosomes in the GnomAD database, including 39,455 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 0.30 ( 7050 hom., cov: 33)

Exomes 𝑓: 0.32 ( 32405 hom. )

Consequence

SSTR2
NM_001050.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.387

Publications

12 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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001050.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR2	NM_001050.3	MANE Select	c.-92-75A>G		intron	N/A	NP_001041.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SSTR2	ENST00000357585.4	TSL:1 MANE Select	c.-92-75A>G	intron	N/A	ENSP00000350198.2
SSTR2	ENST00000579323.5	TSL:4	n.447-75A>G	intron	N/A
ENSG00000264860	ENST00000580671.1	TSL:4	n.312+3865A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45145

AN:

152094

Hom.:

7044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.278

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.0850

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.357

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.342

Gnomad OTH

AF:

0.315

GnomAD4 exome

AF:

0.319

AC:

193757

AN:

607276

Hom.:

32405

AF XY:

0.320

AC XY:

99615

AN XY:

311386

show subpopulations

African (AFR)

AF:

0.233

AC:

3553

AN:

15222

American (AMR)

AF:

0.264

AC:

4958

AN:

18746

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

5352

AN:

14702

East Asian (EAS)

AF:

0.0731

AC:

2324

AN:

31782

South Asian (SAS)

AF:

0.326

AC:

15318

AN:

46936

European-Finnish (FIN)

AF:

0.351

AC:

10493

AN:

29908

Middle Eastern (MID)

AF:

0.301

AC:

694

AN:

2302

European-Non Finnish (NFE)

AF:

0.339

AC:

141213

AN:

416366

Other (OTH)

AF:

0.315

AC:

9852

AN:

31312

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

6682

13364

20047

26729

33411

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2598

5196

7794

10392

12990

<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:

0.297

AC:

45169

AN:

152212

Hom.:

7050

Cov.:

AF XY:

0.297

AC XY:

22108

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.234

AC:

9734

AN:

41532

American (AMR)

AF:

0.268

AC:

4104

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1242

AN:

3472

East Asian (EAS)

AF:

0.0848

AC:

440

AN:

5188

South Asian (SAS)

AF:

0.341

AC:

1644

AN:

4824

European-Finnish (FIN)

AF:

0.357

AC:

3783

AN:

10586

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.342

AC:

23241

AN:

67992

Other (OTH)

AF:

0.312

AC:

659

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1634

3267

4901

6534

8168

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

460

920

1380

1840

2300

<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:

0.301

Hom.:

3805

Bravo

AF:

0.286

Asia WGS

AF:

0.238

AC:

830

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

7.9

(source)

DANN

Benign

0.79

PhyloP100

-0.39

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over