Variant rs34037914 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.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

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=-0.84).

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/exons	MANE	Protein	UniProt
SSTR5	NM_001172560.3 linkuse as main transcript	c.633C>T	p.Phe211Phe	synonymous_variant	2/2	ENST00000689027.1	NP_001166031.1	P35346
SSTR5	NM_001053.4 linkuse as main transcript	c.633C>T	p.Phe211Phe	synonymous_variant	1/1		NP_001044.1	P35346

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1 linkuse as main transcript	c.633C>T	p.Phe211Phe	synonymous_variant	2/2		NM_001172560.3	ENSP00000508487.1		P35346
SSTR5	ENST00000293897.6 linkuse as main transcript	c.633C>T	p.Phe211Phe	synonymous_variant	1/1	6		ENSP00000293897.4		P35346

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

GnomAD3 exomes

AF:

0.0590

AC:

14592

AN:

247184

Hom.:

580

AF XY:

0.0575

AC XY:

7721

AN XY:

134300

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 SAS exome

AF:

0.0458

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

Gnomad4 AFR exome

AF:

0.0113

Gnomad4 AMR exome

AF:

0.103

Gnomad4 ASJ exome

AF:

0.0263

Gnomad4 EAS exome

AF:

0.000782

Gnomad4 SAS exome

AF:

0.0476

Gnomad4 FIN exome

AF:

0.0730

Gnomad4 NFE exome

AF:

0.0666

Gnomad4 OTH exome

AF:

0.0522

GnomAD4 genome

AF:

0.0476

AC:

7257

AN:

152318

Hom.:

236

Cov.:

AF XY:

0.0481

AC XY:

3579

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.0132

Gnomad4 AMR

AF:

0.0670

Gnomad4 ASJ

AF:

0.0277

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.0404

Gnomad4 FIN

AF:

0.0770

Gnomad4 NFE

AF:

0.0650

Gnomad4 OTH

AF:

0.0464

Alfa

AF:

0.0560

Hom.:

142

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

DANN

Benign

0.89

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