dbSNP rs34037914: SSTR5:p.Phe211Phe (chr16-1079501-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001172560.3(SSTR5):c.633C>T(p.Phe211Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 1,611,574 control chromosomes in the GnomAD database, including 3,364 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 0.048 ( 236 hom., cov: 33)

Exomes 𝑓: 0.062 ( 3128 hom. )

Consequence

SSTR5
NM_001172560.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

Publications

8 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-2.4 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR5	NM_001172560.3 link	c.633C>T	p.Phe211Phe	synonymous_variant	Exon 2 of 2	ENST00000689027.1	NP_001166031.1	P35346
SSTR5	NM_001053.4 link	c.633C>T	p.Phe211Phe	synonymous_variant	Exon 1 of 1		NP_001044.1	P35346

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SSTR5	ENST00000689027.1 link	c.633C>T	p.Phe211Phe	synonymous_variant	Exon 2 of 2		NM_001172560.3	ENSP00000508487.1	P35346
SSTR5	ENST00000293897.7 link	c.633C>T	p.Phe211Phe	synonymous_variant	Exon 1 of 1	6		ENSP00000293897.4	P35346
SSTR5	ENST00000711615.1 link	c.633C>T	p.Phe211Phe	synonymous_variant	Exon 2 of 2			ENSP00000518810.1
SSTR5	ENST00000711616.1 link	c.633C>T	p.Phe211Phe	synonymous_variant	Exon 1 of 2			ENSP00000518811.1

Frequencies

GnomAD3 genomes

AF:

0.0476

AC:

7247

AN:

152200

Hom.:

234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0132

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0662

Gnomad ASJ

AF:

0.0277

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0408

Gnomad FIN

AF:

0.0770

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0650

Gnomad OTH

AF:

0.0468

GnomAD2 exomes

AF:

0.0590

AC:

14592

AN:

247184

AF XY:

0.0575

show subpopulations

Gnomad AFR exome

AF:

0.0122

Gnomad AMR exome

AF:

0.108

Gnomad ASJ exome

AF:

0.0259

Gnomad EAS exome

AF:

0.000384

Gnomad FIN exome

AF:

0.0737

Gnomad NFE exome

AF:

0.0641

Gnomad OTH exome

AF:

0.0577

GnomAD4 exome

AF:

0.0624

AC:

91002

AN:

1459256

Hom.:

3128

Cov.:

AF XY:

0.0617

AC XY:

44786

AN XY:

725910

show subpopulations

African (AFR)

AF:

0.0113

AC:

377

AN:

33446

American (AMR)

AF:

0.103

AC:

4595

AN:

44538

Ashkenazi Jewish (ASJ)

AF:

0.0263

AC:

686

AN:

26072

East Asian (EAS)

AF:

0.000782

AC:

AN:

39666

South Asian (SAS)

AF:

0.0476

AC:

4100

AN:

86160

European-Finnish (FIN)

AF:

0.0730

AC:

3797

AN:

52048

Middle Eastern (MID)

AF:

0.0389

AC:

224

AN:

5764

European-Non Finnish (NFE)

AF:

0.0666

AC:

74042

AN:

1111248

Other (OTH)

AF:

0.0522

AC:

3150

AN:

60314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

5897

11794

17690

23587

29484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2740

5480

8220

10960

13700

<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:

0.0476

AC:

7257

AN:

152318

Hom.:

236

Cov.:

AF XY:

0.0481

AC XY:

3579

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0132

AC:

547

AN:

41574

American (AMR)

AF:

0.0670

AC:

1025

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0277

AC:

AN:

3470

East Asian (EAS)

AF:

0.00174

AC:

AN:

5182

South Asian (SAS)

AF:

0.0404

AC:

195

AN:

4828

European-Finnish (FIN)

AF:

0.0770

AC:

818

AN:

10618

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0650

AC:

4422

AN:

68024

Other (OTH)

AF:

0.0464

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

345

690

1036

1381

1726

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0537

Hom.:

178

Bravo

AF:

0.0460

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.0580

EpiControl

AF:

0.0554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.3

(source)

DANN

Benign

0.89

PhyloP100

-2.4

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