Variant chr16-1079193-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001172560.3(SSTR5):c.325C>T(p.Pro109Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 1,612,536 control chromosomes in the GnomAD database, including 2,753 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.065 ( 471 hom., cov: 33)

Exomes 𝑓: 0.047 ( 2282 hom. )

Consequence

SSTR5
NM_001172560.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0021184683).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 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.325C>T	p.Pro109Ser	missense_variant	2/2	ENST00000689027.1	NP_001166031.1	P35346
SSTR5	NM_001053.4 linkuse as main transcript	c.325C>T	p.Pro109Ser	missense_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.325C>T	p.Pro109Ser	missense_variant	2/2		NM_001172560.3	ENSP00000508487.1		P35346
SSTR5	ENST00000293897.6 linkuse as main transcript	c.325C>T	p.Pro109Ser	missense_variant	1/1	6		ENSP00000293897.4		P35346

Frequencies

GnomAD3 genomes

AF:

0.0653

AC:

9933

AN:

152208

Hom.:

472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0440

Gnomad ASJ

AF:

0.0545

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.0303

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0432

Gnomad OTH

AF:

0.0635

GnomAD3 exomes

AF:

0.0527

AC:

13152

AN:

249364

Hom.:

580

AF XY:

0.0567

AC XY:

7687

AN XY:

135478

show subpopulations

Gnomad AFR exome

AF:

0.123

Gnomad AMR exome

AF:

0.0243

Gnomad ASJ exome

AF:

0.0586

Gnomad EAS exome

AF:

0.000872

Gnomad SAS exome

AF:

0.132

Gnomad FIN exome

AF:

0.0330

Gnomad NFE exome

AF:

0.0419

Gnomad OTH exome

AF:

0.0474

GnomAD4 exome

AF:

0.0472

AC:

68984

AN:

1460210

Hom.:

2282

Cov.:

AF XY:

0.0500

AC XY:

36296

AN XY:

726430

show subpopulations

Gnomad4 AFR exome

AF:

0.126

Gnomad4 AMR exome

AF:

0.0275

Gnomad4 ASJ exome

AF:

0.0611

Gnomad4 EAS exome

AF:

0.000403

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.0336

Gnomad4 NFE exome

AF:

0.0407

Gnomad4 OTH exome

AF:

0.0522

GnomAD4 genome

AF:

0.0653

AC:

9943

AN:

152326

Hom.:

471

Cov.:

AF XY:

0.0643

AC XY:

4785

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.0440

Gnomad4 ASJ

AF:

0.0545

Gnomad4 EAS

AF:

0.00289

Gnomad4 SAS

AF:

0.129

Gnomad4 FIN

AF:

0.0303

Gnomad4 NFE

AF:

0.0432

Gnomad4 OTH

AF:

0.0619

Alfa

AF:

0.0457

Hom.:

201

Bravo

AF:

0.0666

TwinsUK

AF:

0.0442

AC:

164

ALSPAC

AF:

0.0402

AC:

155

ESP6500AA

AF:

0.115

AC:

505

ESP6500EA

AF:

0.0394

AC:

339

ExAC

AF:

0.0566

AC:

6835

Asia WGS

AF:

0.0490

AC:

171

AN:

3478

EpiCase

AF:

0.0411

EpiControl

AF:

0.0453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.86

DANN

Benign

0.89

DEOGEN2

Benign

0.067

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.058

LIST_S2

Uncertain

0.88

MetaRNN

Benign

0.0021

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.1

PrimateAI

Benign

0.28

PROVEAN

Benign

2.6

REVEL

Benign

0.10

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.034

MPC

0.23

ClinPred

0.00028

GERP RS

0.41

Varity_R

0.049

gMVP

0.17

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