16-1079872-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001172560.3(SSTR5):c.1004C>T(p.Pro335Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 1,609,844 control chromosomes in the GnomAD database, including 237,566 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 20002 hom., cov: 35)

Exomes 𝑓: 0.54 ( 217564 hom. )

Consequence

SSTR5
NM_001172560.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.117

Publications

43 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.4184657E-6).

BP6

Variant 16-1079872-C-T is Benign according to our data. Variant chr16-1079872-C-T is described in ClinVar as Benign. ClinVar VariationId is 1248656.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	NM_001172560.3	MANE Select	c.1004C>T	p.Pro335Leu	missense	Exon 2 of 2	NP_001166031.1
	SSTR5	NM_001053.4		c.1004C>T	p.Pro335Leu	missense	Exon 1 of 1	NP_001044.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SSTR5	ENST00000689027.1	MANE Select	c.1004C>T	p.Pro335Leu	missense	Exon 2 of 2	ENSP00000508487.1
SSTR5	ENST00000293897.7	TSL:6	c.1004C>T	p.Pro335Leu	missense	Exon 1 of 1	ENSP00000293897.4
SSTR5	ENST00000711615.1		c.1004C>T	p.Pro335Leu	missense	Exon 2 of 2	ENSP00000518810.1

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76349

AN:

152048

Hom.:

19994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.671

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.613

Gnomad EAS

AF:

0.808

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.603

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.512

GnomAD2 exomes

AF:

0.543

AC:

132664

AN:

244142

AF XY:

0.539

show subpopulations

Gnomad AFR exome

AF:

0.371

Gnomad AMR exome

AF:

0.555

Gnomad ASJ exome

AF:

0.581

Gnomad EAS exome

AF:

0.807

Gnomad FIN exome

AF:

0.592

Gnomad NFE exome

AF:

0.538

Gnomad OTH exome

AF:

0.562

GnomAD4 exome

AF:

0.542

AC:

790044

AN:

1457678

Hom.:

217564

Cov.:

AF XY:

0.539

AC XY:

390848

AN XY:

725198

show subpopulations

African (AFR)

AF:

0.358

AC:

11973

AN:

33454

American (AMR)

AF:

0.550

AC:

24497

AN:

44526

Ashkenazi Jewish (ASJ)

AF:

0.577

AC:

15045

AN:

26090

East Asian (EAS)

AF:

0.825

AC:

32724

AN:

39644

South Asian (SAS)

AF:

0.434

AC:

37371

AN:

86182

European-Finnish (FIN)

AF:

0.594

AC:

30135

AN:

50774

Middle Eastern (MID)

AF:

0.524

AC:

3019

AN:

5766

European-Non Finnish (NFE)

AF:

0.542

AC:

601982

AN:

1110982

Other (OTH)

AF:

0.553

AC:

33298

AN:

60260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

22404

44807

67211

89614

112018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17074

34148

51222

68296

85370

<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:

0.502

AC:

76397

AN:

152166

Hom.:

20002

Cov.:

AF XY:

0.504

AC XY:

37487

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.375

AC:

15561

AN:

41518

American (AMR)

AF:

0.502

AC:

7687

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

2127

AN:

3472

East Asian (EAS)

AF:

0.807

AC:

4172

AN:

5168

South Asian (SAS)

AF:

0.453

AC:

2184

AN:

4824

European-Finnish (FIN)

AF:

0.603

AC:

6395

AN:

10610

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.536

AC:

36444

AN:

67952

Other (OTH)

AF:

0.510

AC:

1078

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1971

3941

5912

7882

9853

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

682

1364

2046

2728

3410

<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:

0.533

Hom.:

48906

Bravo

AF:

0.495

TwinsUK

AF:

0.539

AC:

2000

ALSPAC

AF:

0.532

AC:

2052

ESP6500AA

AF:

0.383

AC:

1671

ESP6500EA

AF:

0.539

AC:

4627

ExAC

AF:

0.532

AC:

63977

Asia WGS

AF:

0.620

AC:

2153

AN:

3478

ClinVar

Significance: 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:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Oct 01, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 21249361)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.070

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.68

FATHMM_MKL

Benign

0.090

LIST_S2

Benign

0.55

MetaRNN

Benign

0.0000014

MetaSVM

Benign

-0.97

MutationAssessor

Benign

1.6

PhyloP100

0.12

PrimateAI

Benign

0.33

PROVEAN

Benign

-1.3

REVEL

Benign

0.078

Sift

Benign

0.17

Sift4G

Benign

0.45

Polyphen

0.055

Vest4

0.038

MPC

0.24

ClinPred

0.0048

GERP RS

2.2

Varity_R

0.029

gMVP

0.34

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over