Genetic Variant SSTR5:c.-27-436C>T (chr16-1078406-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001172560.3(SSTR5):c.-27-436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 175,934 control chromosomes in the GnomAD database, including 12,220 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 0.35 ( 10359 hom., cov: 33)

Exomes 𝑓: 0.37 ( 1861 hom. )

Consequence

SSTR5
NM_001172560.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.584

Publications

11 publications found

Variant links:

Genes affected

SSTR5 (HGNC:11334): (somatostatin receptor 5) Somatostatin and its related peptide cortistatin exert multiple biological actions on normal and tumoral tissue targets by interacting with somatostatin receptors (SSTRs). The protein encoded by this gene is one of the SSTRs, which is a multi-pass membrane protein and belongs to the G-protein coupled receptor 1 family. The activity of this receptor is mediated by G proteins which inhibit adenylyl cyclase, and different regions of this receptor molecule are required for the activation of different signaling pathways. A mutation in this gene results in somatostatin analog resistance. Alternatively spliced transcript variants have been identified in this gene.[provided by RefSeq, Feb 2010]

SSTR5 links:

SSTR5-AS1 (HGNC:26502): (SSTR5 antisense RNA 1)

SSTR5-AS1 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172560.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	NM_001172560.3	MANE Select	c.-27-436C>T		intron	N/A	NP_001166031.1	P35346
	SSTR5-AS1	NR_027242.1		n.274+52G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SSTR5	ENST00000689027.1	MANE Select	c.-27-436C>T	intron	N/A	ENSP00000508487.1	P35346
SSTR5	ENST00000711615.1		c.-27-436C>T	intron	N/A	ENSP00000518810.1	P35346
SSTR5	ENST00000886519.1		c.-27-436C>T	intron	N/A	ENSP00000556578.1

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52941

AN:

152006

Hom.:

10361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.369

GnomAD4 exome

AF:

0.367

AC:

8732

AN:

23810

Hom.:

1861

Cov.:

AF XY:

0.369

AC XY:

4483

AN XY:

12140

show subpopulations

African (AFR)

AF:

0.183

AC:

AN:

442

American (AMR)

AF:

0.396

AC:

1268

AN:

3202

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

148

AN:

434

East Asian (EAS)

AF:

0.105

AC:

171

AN:

1630

South Asian (SAS)

AF:

0.341

AC:

660

AN:

1936

European-Finnish (FIN)

AF:

0.388

AC:

255

AN:

658

Middle Eastern (MID)

AF:

0.338

AC:

AN:

European-Non Finnish (NFE)

AF:

0.403

AC:

5734

AN:

14234

Other (OTH)

AF:

0.325

AC:

392

AN:

1206

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

243

485

728

970

1213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

188

282

376

470

<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:

0.348

AC:

52954

AN:

152124

Hom.:

10359

Cov.:

AF XY:

0.350

AC XY:

26069

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.181

AC:

7537

AN:

41530

American (AMR)

AF:

0.427

AC:

6529

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

1138

AN:

3470

East Asian (EAS)

AF:

0.122

AC:

627

AN:

5154

South Asian (SAS)

AF:

0.331

AC:

1598

AN:

4824

European-Finnish (FIN)

AF:

0.470

AC:

4990

AN:

10610

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.431

AC:

29263

AN:

67942

Other (OTH)

AF:

0.366

AC:

773

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1708

3415

5123

6830

8538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<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:

0.407

Hom.:

19019

Bravo

AF:

0.337

Asia WGS

AF:

0.236

AC:

823

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.1

(source)

DANN

Benign

0.63

PhyloP100

-0.58

PromoterAI

-0.0087

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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