Genetic Variant SSTR5:p.Phe107Phe (chr16-1079189-C-T) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_001172560.3(SSTR5):c.321C>T(p.Phe107Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,612,558 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0044 ( 16 hom. )

Consequence

SSTR5
NM_001172560.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.96

Publications

2 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 16-1079189-C-T is Benign according to our data. Variant chr16-1079189-C-T is described in ClinVar as Benign. ClinVar VariationId is 771197.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.96 with no splicing effect.

BS2

High AC in GnomAd4 at 582 AD gene.

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.321C>T	p.Phe107Phe	synonymous	Exon 2 of 2	NP_001166031.1	P35346
	SSTR5	NM_001053.4		c.321C>T	p.Phe107Phe	synonymous	Exon 1 of 1	NP_001044.1	P35346

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SSTR5	ENST00000689027.1	MANE Select	c.321C>T	p.Phe107Phe	synonymous	Exon 2 of 2	ENSP00000508487.1	P35346
SSTR5	ENST00000293897.7	TSL:6	c.321C>T	p.Phe107Phe	synonymous	Exon 1 of 1	ENSP00000293897.4	P35346
SSTR5	ENST00000711615.1		c.321C>T	p.Phe107Phe	synonymous	Exon 2 of 2	ENSP00000518810.1	P35346

Frequencies

GnomAD3 genomes

AF:

0.00382

AC:

582

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000651

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00791

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00545

Gnomad OTH

AF:

0.00526

GnomAD2 exomes

AF:

0.00412

AC:

1028

AN:

249392

AF XY:

0.00418

show subpopulations

Gnomad AFR exome

AF:

0.000560

Gnomad AMR exome

AF:

0.00440

Gnomad ASJ exome

AF:

0.00421

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.00409

Gnomad NFE exome

AF:

0.00599

Gnomad OTH exome

AF:

0.00657

GnomAD4 exome

AF:

0.00438

AC:

6401

AN:

1460194

Hom.:

Cov.:

AF XY:

0.00435

AC XY:

3163

AN XY:

726420

show subpopulations

African (AFR)

AF:

0.000627

AC:

AN:

33470

American (AMR)

AF:

0.00472

AC:

211

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.00463

AC:

121

AN:

26118

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39690

South Asian (SAS)

AF:

0.000835

AC:

AN:

86250

European-Finnish (FIN)

AF:

0.00443

AC:

230

AN:

51926

Middle Eastern (MID)

AF:

0.00763

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00486

AC:

5404

AN:

1111900

Other (OTH)

AF:

0.00490

AC:

296

AN:

60360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

463

926

1390

1853

2316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

194

388

582

776

970

<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:

0.00382

AC:

582

AN:

152364

Hom.:

Cov.:

AF XY:

0.00365

AC XY:

272

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.000649

AC:

AN:

41596

American (AMR)

AF:

0.00790

AC:

121

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.00490

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5188

South Asian (SAS)

AF:

0.000621

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00273

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00545

AC:

371

AN:

68020

Other (OTH)

AF:

0.00521

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

123

154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00234

Hom.:

Bravo

AF:

0.00442

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00649

EpiControl

AF:

0.00729

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

5.9

(source)

DANN

Benign

0.90

PhyloP100

-2.0

PromoterAI

0.012

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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