NM_001172560.3:c.142C>A

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.142C>A(p.Leu48Met) 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 1,601,838 control chromosomes in the GnomAD database, including 2,199 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 144 hom., cov: 33)

Exomes 𝑓: 0.050 ( 2055 hom. )

Consequence

SSTR5
NM_001172560.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0830

Publications

28 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:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.0033727884).

BP6

Variant 16-1079010-C-A is Benign according to our data. Variant chr16-1079010-C-A is described in ClinVar as Benign. ClinVar VariationId is 1224021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	NM_001172560.3	MANE Select	c.142C>A	p.Leu48Met	missense	Exon 2 of 2	NP_001166031.1	P35346
	SSTR5	NM_001053.4		c.142C>A	p.Leu48Met	missense	Exon 1 of 1	NP_001044.1	P35346

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SSTR5	ENST00000689027.1	MANE Select	c.142C>A	p.Leu48Met	missense	Exon 2 of 2	ENSP00000508487.1	P35346
SSTR5	ENST00000293897.7	TSL:6	c.142C>A	p.Leu48Met	missense	Exon 1 of 1	ENSP00000293897.4	P35346
SSTR5	ENST00000711615.1		c.142C>A	p.Leu48Met	missense	Exon 2 of 2	ENSP00000518810.1	P35346

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

5615

AN:

152218

Hom.:

143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0108

Gnomad AMI

AF:

0.0912

Gnomad AMR

AF:

0.0429

Gnomad ASJ

AF:

0.0446

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.0189

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0573

Gnomad OTH

AF:

0.0435

GnomAD2 exomes

AF:

0.0374

AC:

8533

AN:

228194

AF XY:

0.0380

show subpopulations

Gnomad AFR exome

AF:

0.00982

Gnomad AMR exome

AF:

0.0280

Gnomad ASJ exome

AF:

0.0408

Gnomad EAS exome

AF:

0.000179

Gnomad FIN exome

AF:

0.0203

Gnomad NFE exome

AF:

0.0591

Gnomad OTH exome

AF:

0.0418

GnomAD4 exome

AF:

0.0501

AC:

72672

AN:

1449502

Hom.:

2055

Cov.:

AF XY:

0.0493

AC XY:

35515

AN XY:

720492

show subpopulations

African (AFR)

AF:

0.00880

AC:

292

AN:

33168

American (AMR)

AF:

0.0299

AC:

1288

AN:

43008

Ashkenazi Jewish (ASJ)

AF:

0.0447

AC:

1159

AN:

25956

East Asian (EAS)

AF:

0.000205

AC:

AN:

38932

South Asian (SAS)

AF:

0.0178

AC:

1524

AN:

85392

European-Finnish (FIN)

AF:

0.0199

AC:

995

AN:

50064

Middle Eastern (MID)

AF:

0.0592

AC:

340

AN:

5748

European-Non Finnish (NFE)

AF:

0.0582

AC:

64434

AN:

1107330

Other (OTH)

AF:

0.0439

AC:

2632

AN:

59904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

4659

9319

13978

18638

23297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2332

4664

6996

9328

11660

<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:

0.0369

AC:

5618

AN:

152336

Hom.:

144

Cov.:

AF XY:

0.0349

AC XY:

2598

AN XY:

74492

show subpopulations

African (AFR)

AF:

0.0107

AC:

447

AN:

41584

American (AMR)

AF:

0.0429

AC:

656

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0446

AC:

155

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.0149

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.0189

AC:

201

AN:

10630

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0573

AC:

3895

AN:

68008

Other (OTH)

AF:

0.0430

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

289

577

866

1154

1443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0483

Hom.:

248

Bravo

AF:

0.0377

TwinsUK

AF:

0.0542

AC:

201

ALSPAC

AF:

0.0607

AC:

234

ESP6500AA

AF:

0.0115

AC:

ESP6500EA

AF:

0.0548

AC:

470

ExAC

AF:

0.0346

AC:

4153

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.070

Eigen

Benign

-0.0064

Eigen_PC

Benign

-0.12

FATHMM_MKL

Benign

0.74

LIST_S2

Benign

0.69

MetaRNN

Benign

0.0034

MetaSVM

Benign

-1.1

MutationAssessor

Benign

2.0

PhyloP100

0.083

PrimateAI

Uncertain

0.62

PROVEAN

Benign

-0.80

REVEL

Benign

0.091

Sift

Benign

0.11

Sift4G

Benign

0.21

Polyphen

0.93

Vest4

0.14

MPC

0.81

ClinPred

0.010

GERP RS

1.4

PromoterAI

0.079

Neutral

(source)

Varity_R

0.085

gMVP

0.29

Mutation Taster

=92/8

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

Computational scores

Splicing

Publications

Other links and lift over