dbSNP rs1466113: SSTR2:c.-92-49C>G (chr17-73169179-C-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.-92-49C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,054,650 control chromosomes in the GnomAD database, including 192,653 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 0.64 ( 31600 hom., cov: 33)

Exomes 𝑓: 0.60 ( 161053 hom. )

Consequence

SSTR2
NM_001050.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415

Publications

19 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 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.-92-49C>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.-92-49C>G	intron	N/A	ENSP00000350198.2
SSTR2	ENST00000579323.5	TSL:4	n.447-49C>G	intron	N/A
ENSG00000264860	ENST00000580671.1	TSL:4	n.312+3891C>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

97218

AN:

151990

Hom.:

31557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.641

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.549

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.586

Gnomad OTH

AF:

0.648

GnomAD4 exome

AF:

0.595

AC:

537448

AN:

902542

Hom.:

161053

Cov.:

AF XY:

0.599

AC XY:

269261

AN XY:

449618

show subpopulations

African (AFR)

AF:

0.758

AC:

15675

AN:

20682

American (AMR)

AF:

0.685

AC:

13236

AN:

19328

Ashkenazi Jewish (ASJ)

AF:

0.651

AC:

10818

AN:

16610

East Asian (EAS)

AF:

0.573

AC:

18924

AN:

33046

South Asian (SAS)

AF:

0.704

AC:

37958

AN:

53888

European-Finnish (FIN)

AF:

0.551

AC:

17046

AN:

30922

Middle Eastern (MID)

AF:

0.635

AC:

1818

AN:

2862

European-Non Finnish (NFE)

AF:

0.580

AC:

396942

AN:

684312

Other (OTH)

AF:

0.612

AC:

25031

AN:

40892

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

11027

22053

33080

44106

55133

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9836

19672

29508

39344

49180

<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:

0.640

AC:

97306

AN:

152108

Hom.:

31600

Cov.:

AF XY:

0.639

AC XY:

47529

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.749

AC:

31069

AN:

41504

American (AMR)

AF:

0.660

AC:

10095

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.641

AC:

2227

AN:

3472

East Asian (EAS)

AF:

0.527

AC:

2722

AN:

5166

South Asian (SAS)

AF:

0.714

AC:

3442

AN:

4824

European-Finnish (FIN)

AF:

0.549

AC:

5804

AN:

10570

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.586

AC:

39802

AN:

67964

Other (OTH)

AF:

0.644

AC:

1360

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1798

3596

5395

7193

8991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<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:

0.513

Hom.:

1474

Bravo

AF:

0.652

Asia WGS

AF:

0.663

AC:

2305

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.3

(source)

DANN

Benign

0.28

PhyloP100

-0.41

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