Genetic Variant SST:c.*22A>G (chr3-187669043-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_001048.4(SST):c.*22A>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 0.0948 in 1,612,634 control chromosomes in the GnomAD database, including 7,878 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 0.12 ( 1096 hom., cov: 32)

Exomes 𝑓: 0.093 ( 6782 hom. )

Consequence

SST
NM_001048.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.653

Variant links:

Genes affected

SST (HGNC:11329): (somatostatin) The hormone somatostatin has active 14 aa and 28 aa forms that are produced by alternate cleavage of the single preproprotein encoded by this gene. Somatostatin is expressed throughout the body and inhibits the release of numerous secondary hormones by binding to high-affinity G-protein-coupled somatostatin receptors. This hormone is an important regulator of the endocrine system through its interactions with pituitary growth hormone, thyroid stimulating hormone, and most hormones of the gastrointestinal tract. Somatostatin also affects rates of neurotransmission in the central nervous system and proliferation of both normal and tumorigenic cells. [provided by RefSeq, Jul 2008]

SST 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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SST	NM_001048.4 link	c.*22A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000287641.4	NP_001039.1	P61278

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SST	ENST00000287641 link	c.*22A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_001048.4	ENSP00000287641.3		P61278

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17661

AN:

151908

Hom.:

1095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.0571

Gnomad SAS

AF:

0.0737

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0890

Gnomad OTH

AF:

0.107

GnomAD2 exomes

AF:

0.109

AC:

27506

AN:

251394

AF XY:

0.104

show subpopulations

Gnomad AFR exome

AF:

0.151

Gnomad AMR exome

AF:

0.186

Gnomad ASJ exome

AF:

0.115

Gnomad EAS exome

AF:

0.0561

Gnomad FIN exome

AF:

0.147

Gnomad NFE exome

AF:

0.0906

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.0925

AC:

135153

AN:

1460608

Hom.:

6782

Cov.:

AF XY:

0.0919

AC XY:

66759

AN XY:

726710

show subpopulations

Gnomad4 AFR exome

AF:

0.150

AC:

5012

AN:

33458

Gnomad4 AMR exome

AF:

0.189

AC:

8450

AN:

44724

Gnomad4 ASJ exome

AF:

0.118

AC:

3072

AN:

26126

Gnomad4 EAS exome

AF:

0.0609

AC:

2416

AN:

39694

Gnomad4 SAS exome

AF:

0.0767

AC:

6612

AN:

86238

Gnomad4 FIN exome

AF:

0.142

AC:

7555

AN:

53330

Gnomad4 NFE exome

AF:

0.0860

AC:

95515

AN:

1110932

Gnomad4 Remaining exome

AF:

0.0966

AC:

5828

AN:

60346

Heterozygous variant carriers

6888

13776

20665

27553

34441

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

3584

7168

10752

14336

17920

<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:

0.116

AC:

17670

AN:

152026

Hom.:

1096

Cov.:

AF XY:

0.119

AC XY:

8841

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.143

AC:

0.142881

AN:

0.142881

Gnomad4 AMR

AF:

0.168

AC:

0.16754

AN:

0.16754

Gnomad4 ASJ

AF:

0.118

AC:

0.117867

AN:

0.117867

Gnomad4 EAS

AF:

0.0565

AC:

0.0565015

AN:

0.0565015

Gnomad4 SAS

AF:

0.0738

AC:

0.0737739

AN:

0.0737739

Gnomad4 FIN

AF:

0.156

AC:

0.155977

AN:

0.155977

Gnomad4 NFE

AF:

0.0890

AC:

0.0889863

AN:

0.0889863

Gnomad4 OTH

AF:

0.107

AC:

0.107211

AN:

0.107211

Heterozygous variant carriers

786

1572

2359

3145

3931

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.103

Hom.:

1183

Bravo

AF:

0.121

Asia WGS

AF:

0.0880

AC:

310

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.43

DANN

Benign

0.33

Mutation Taster

=100/0

polymorphism (auto)

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over