dbSNP rs229566: SSTR3:c.*456C>T (chr22-37206091-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001051.5(SSTR3):c.*456C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 156,590 control chromosomes in the GnomAD database, including 12,314 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 0.39 ( 12051 hom., cov: 32)

Exomes 𝑓: 0.31 ( 263 hom. )

Consequence

SSTR3
NM_001051.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.572

Publications

13 publications found

Variant links:

Genes affected

SSTR3 (HGNC:11332): (somatostatin receptor 3) This gene encodes a member of the somatostatin receptor protein family. Somatostatins are peptide hormones that regulate diverse cellular functions such as neurotransmission, cell proliferation, and endocrine signaling as well as inhibiting the release of many hormones and other secretory proteins. Somatostatin has two active forms of 14 and 28 amino acids. The biological effects of somatostatins are mediated by a family of G-protein coupled somatostatin receptors that are expressed in a tissue-specific manner. Somatostatin receptors form homodimers and heterodimers with other members of the superfamily as well as with other G-protein coupled receptors and receptor tyrosine kinases. This protein is functionally coupled to adenylyl cyclase. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

SSTR3 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 = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR3	NM_001051.5 link	c.*456C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000610913.2	NP_001042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR3	ENST00000610913.2 link	c.*456C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001051.5	ENSP00000480971.1

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59030

AN:

151912

Hom.:

12030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.361

GnomAD4 exome

AF:

0.305

AC:

1392

AN:

4560

Hom.:

263

Cov.:

AF XY:

0.304

AC XY:

726

AN XY:

2388

show subpopulations

African (AFR)

AF:

0.396

AC:

AN:

106

American (AMR)

AF:

0.267

AC:

AN:

300

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

AN:

122

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.313

AC:

AN:

166

European-Finnish (FIN)

AF:

0.235

AC:

AN:

162

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.312

AC:

1044

AN:

3350

Other (OTH)

AF:

0.340

AC:

AN:

262

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

122

163

204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.389

AC:

59100

AN:

152030

Hom.:

12051

Cov.:

AF XY:

0.382

AC XY:

28387

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.533

AC:

22092

AN:

41422

American (AMR)

AF:

0.361

AC:

5516

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.265

AC:

921

AN:

3470

East Asian (EAS)

AF:

0.244

AC:

1261

AN:

5162

South Asian (SAS)

AF:

0.379

AC:

1830

AN:

4824

European-Finnish (FIN)

AF:

0.284

AC:

3006

AN:

10590

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.344

AC:

23346

AN:

67948

Other (OTH)

AF:

0.362

AC:

767

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1814

3628

5441

7255

9069

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

554

1108

1662

2216

2770

<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:

0.376

Hom.:

2560

Bravo

AF:

0.397

Asia WGS

AF:

0.346

AC:

1201

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

0.48

(source)

DANN

Benign

0.41

PhyloP100

-0.57

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