Genetic Variant NM_001172560.3:c.26C>T (chr16-1078894-C-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001172560.3(SSTR5):c.26C>T(p.Thr9Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000929 in 1,606,448 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0023 ( 4 hom., cov: 33)

Exomes 𝑓: 0.00079 ( 4 hom. )

Consequence

SSTR5
NM_001172560.3 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.38

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 made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004814476).

BP6

Variant 16-1078894-C-T is Benign according to our data. Variant chr16-1078894-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 778999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 348 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR5	NM_001172560.3 link	c.26C>T	p.Thr9Met	missense_variant	Exon 2 of 2	ENST00000689027.1	NP_001166031.1	P35346
SSTR5	NM_001053.4 link	c.26C>T	p.Thr9Met	missense_variant	Exon 1 of 1		NP_001044.1	P35346
SSTR5-AS1	NR_027242.1 link	n.-163G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1 link	c.26C>T	p.Thr9Met	missense_variant	Exon 2 of 2		NM_001172560.3	ENSP00000508487.1		P35346

Frequencies

GnomAD3 genomes

AF:

0.00228

AC:

347

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00302

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00981

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000966

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000794

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00136

AC:

318

AN:

234020

Hom.:

AF XY:

0.00119

AC XY:

154

AN XY:

129006

show subpopulations

Gnomad AFR exome

AF:

0.00276

Gnomad AMR exome

AF:

0.00367

Gnomad ASJ exome

AF:

0.00114

Gnomad EAS exome

AF:

0.00140

Gnomad SAS exome

AF:

0.000299

Gnomad FIN exome

AF:

0.000116

Gnomad NFE exome

AF:

0.000914

Gnomad OTH exome

AF:

0.00190

GnomAD4 exome

AF:

0.000787

AC:

1144

AN:

1454138

Hom.:

Cov.:

AF XY:

0.000732

AC XY:

530

AN XY:

723562

show subpopulations

Gnomad4 AFR exome

AF:

0.00314

Gnomad4 AMR exome

AF:

0.00390

Gnomad4 ASJ exome

AF:

0.000614

Gnomad4 EAS exome

AF:

0.000732

Gnomad4 SAS exome

AF:

0.000198

Gnomad4 FIN exome

AF:

0.0000418

Gnomad4 NFE exome

AF:

0.000598

Gnomad4 OTH exome

AF:

0.00201

GnomAD4 genome

AF:

0.00228

AC:

348

AN:

152310

Hom.:

Cov.:

AF XY:

0.00240

AC XY:

179

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00301

Gnomad4 AMR

AF:

0.00980

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000969

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000794

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00134

Hom.:

Bravo

AF:

0.00276

ESP6500AA

AF:

0.00163

AC:

ESP6500EA

AF:

0.000707

AC:

ExAC

AF:

0.00104

AC:

124

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00115

EpiControl

AF:

0.00125

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.56

CADD

Benign

4.7

DANN

Benign

0.90

DEOGEN2

Benign

0.044

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0032

LIST_S2

Benign

0.26

MetaRNN

Benign

0.0048

MetaSVM

Benign

-0.83

MutationAssessor

Benign

1.4

PrimateAI

Benign

0.44

PROVEAN

Benign

-0.23

REVEL

Benign

0.14

Sift

Benign

0.19

Sift4G

Benign

0.17

Polyphen

0.66

Vest4

0.10

MVP

0.41

MPC

0.23

ClinPred

0.0028

GERP RS

-6.4

Varity_R

0.015

gMVP

0.39

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over