dbSNP rs4988479: SSTR5:p.Thr9Thr (chr16-1078895-G-A) – 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.27G>A(p.Thr9Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00948 in 1,606,246 control chromosomes in the GnomAD database, including 252 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 0.0073 ( 21 hom., cov: 33)

Exomes 𝑓: 0.0097 ( 231 hom. )

Consequence

SSTR5
NM_001172560.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75

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:

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

SSTR5-AS1 links:

Genome browser will be placed here

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=-0.76).

BP7

Synonymous conserved (PhyloP=-1.75 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0565 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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SSTR5	NM_001172560.3	MANE Select	c.27G>A	p.Thr9Thr	synonymous	Exon 2 of 2	NP_001166031.1	P35346
SSTR5	NM_001053.4		c.27G>A	p.Thr9Thr	synonymous	Exon 1 of 1	NP_001044.1	P35346
SSTR5-AS1	NR_027242.1		n.-164C>T		upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SSTR5	ENST00000689027.1	MANE Select	c.27G>A	p.Thr9Thr	synonymous	Exon 2 of 2	ENSP00000508487.1	P35346
SSTR5	ENST00000293897.7	TSL:6	c.27G>A	p.Thr9Thr	synonymous	Exon 1 of 1	ENSP00000293897.4	P35346
SSTR5	ENST00000711615.1		c.27G>A	p.Thr9Thr	synonymous	Exon 2 of 2	ENSP00000518810.1	P35346

Frequencies

GnomAD3 genomes

AF:

0.00730

AC:

1111

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00948

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00155

Gnomad SAS

AF:

0.0549

Gnomad FIN

AF:

0.00886

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00772

Gnomad OTH

AF:

0.00957

GnomAD2 exomes

AF:

0.0128

AC:

3003

AN:

233704

AF XY:

0.0154

show subpopulations

Gnomad AFR exome

AF:

0.000921

Gnomad AMR exome

AF:

0.00625

Gnomad ASJ exome

AF:

0.00290

Gnomad EAS exome

AF:

0.000559

Gnomad FIN exome

AF:

0.00958

Gnomad NFE exome

AF:

0.00655

Gnomad OTH exome

AF:

0.0102

GnomAD4 exome

AF:

0.00971

AC:

14114

AN:

1453986

Hom.:

231

Cov.:

AF XY:

0.0111

AC XY:

8060

AN XY:

723486

show subpopulations

African (AFR)

AF:

0.00129

AC:

AN:

33390

American (AMR)

AF:

0.00677

AC:

302

AN:

44580

Ashkenazi Jewish (ASJ)

AF:

0.00315

AC:

AN:

26062

East Asian (EAS)

AF:

0.000252

AC:

AN:

39618

South Asian (SAS)

AF:

0.0578

AC:

4973

AN:

85974

European-Finnish (FIN)

AF:

0.0115

AC:

552

AN:

47890

Middle Eastern (MID)

AF:

0.00507

AC:

AN:

5322

European-Non Finnish (NFE)

AF:

0.00682

AC:

7582

AN:

1111074

Other (OTH)

AF:

0.00904

AC:

543

AN:

60076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

888

1776

2665

3553

4441

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.00727

AC:

1107

AN:

152260

Hom.:

Cov.:

AF XY:

0.00826

AC XY:

615

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.00101

AC:

AN:

41570

American (AMR)

AF:

0.00947

AC:

145

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.00260

AC:

AN:

3468

East Asian (EAS)

AF:

0.00155

AC:

AN:

5154

South Asian (SAS)

AF:

0.0541

AC:

261

AN:

4826

European-Finnish (FIN)

AF:

0.00886

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00772

AC:

525

AN:

68000

Other (OTH)

AF:

0.00947

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

108

161

215

269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.00641

Hom.:

Bravo

AF:

0.00531

Asia WGS

AF:

0.0260

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

3.3

(source)

DANN

Benign

0.68

PhyloP100

-1.8

PromoterAI

0.00040

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over