Variant rs4988479 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001172560.3(SSTR5):c.27G>A(p.Thr9=) 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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSTR5	NM_001172560.3 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	2/2	ENST00000689027.1	NP_001166031.1
SSTR5	NM_001053.4 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	1/1		NP_001044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	Appris
SSTR5	ENST00000689027.1 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	2/2	NM_001172560.3	ENSP00000508487	P1
SSTR5	ENST00000293897.7 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	1/1		ENSP00000293897	P1
SSTR5	ENST00000711615.1 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	2/2		ENSP00000518810	P1
SSTR5	ENST00000711616.1 linkuse as main transcript	c.27G>A	p.Thr9=	synonymous_variant	1/2		ENSP00000518811

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

GnomAD3 exomes

AF:

0.0128

AC:

3003

AN:

233704

Hom.:

AF XY:

0.0154

AC XY:

1984

AN XY:

128840

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 SAS exome

AF:

0.0607

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

Gnomad4 AFR exome

AF:

0.00129

Gnomad4 AMR exome

AF:

0.00677

Gnomad4 ASJ exome

AF:

0.00315

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0578

Gnomad4 FIN exome

AF:

0.0115

Gnomad4 NFE exome

AF:

0.00682

Gnomad4 OTH exome

AF:

0.00904

GnomAD4 genome

AF:

0.00727

AC:

1107

AN:

152260

Hom.:

Cov.:

AF XY:

0.00826

AC XY:

615

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00947

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.0541

Gnomad4 FIN

AF:

0.00886

Gnomad4 NFE

AF:

0.00772

Gnomad4 OTH

AF:

0.00947

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

3.3

DANN

Benign

0.68

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