16-1078894-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -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. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T9A) has been classified as Uncertain significance.

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

Publications

2 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:

SSTR5-AS1 (HGNC:26502): (SSTR5 antisense RNA 1)

SSTR5-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 778999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 348 AD gene.

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SSTR5	NM_001172560.3	MANE Select	c.26C>T	p.Thr9Met	missense	Exon 2 of 2	NP_001166031.1	P35346
SSTR5	NM_001053.4		c.26C>T	p.Thr9Met	missense	Exon 1 of 1	NP_001044.1	P35346
SSTR5-AS1	NR_027242.1		n.-163G>A		upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SSTR5	ENST00000689027.1	MANE Select	c.26C>T	p.Thr9Met	missense	Exon 2 of 2	ENSP00000508487.1	P35346
SSTR5	ENST00000293897.7	TSL:6	c.26C>T	p.Thr9Met	missense	Exon 1 of 1	ENSP00000293897.4	P35346
SSTR5	ENST00000711615.1		c.26C>T	p.Thr9Met	missense	Exon 2 of 2	ENSP00000518810.1	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

GnomAD2 exomes

AF:

0.00136

AC:

318

AN:

234020

AF XY:

0.00119

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 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

African (AFR)

AF:

0.00314

AC:

105

AN:

33402

American (AMR)

AF:

0.00390

AC:

174

AN:

44598

Ashkenazi Jewish (ASJ)

AF:

0.000614

AC:

AN:

26058

East Asian (EAS)

AF:

0.000732

AC:

AN:

39636

South Asian (SAS)

AF:

0.000198

AC:

AN:

85970

European-Finnish (FIN)

AF:

0.0000418

AC:

AN:

47898

Middle Eastern (MID)

AF:

0.00280

AC:

AN:

5352

European-Non Finnish (NFE)

AF:

0.000598

AC:

665

AN:

1111120

Other (OTH)

AF:

0.00201

AC:

121

AN:

60104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

130

196

261

326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.00228

AC:

348

AN:

152310

Hom.:

Cov.:

AF XY:

0.00240

AC XY:

179

AN XY:

74482

show subpopulations

African (AFR)

AF:

0.00301

AC:

125

AN:

41570

American (AMR)

AF:

0.00980

AC:

150

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3472

East Asian (EAS)

AF:

0.000969

AC:

AN:

5162

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000794

AC:

AN:

68032

Other (OTH)

AF:

0.00426

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00134

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

ClinVar submissions as Germline

Significance:Likely 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

0.16

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.56

CADD

Benign

4.7

(source)

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

PhyloP100

-2.4

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

PromoterAI

-0.037

Neutral

(source)

Varity_R

0.015

gMVP

0.39

Mutation Taster

=100/0

polymorphism

(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