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GeneBe

16-1079024-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001172560.3(SSTR5):c.156G>A(p.Ala52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,606,548 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 5 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 17 hom. )

Consequence

SSTR5
NM_001172560.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.79
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-1079024-G-A is Benign according to our data. Variant chr16-1079024-G-A is described in ClinVar as [Benign]. Clinvar id is 3035294.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-4.79 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 329 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SSTR5NM_001172560.3 linkuse as main transcriptc.156G>A p.Ala52= synonymous_variant 2/2 ENST00000689027.1
SSTR5NM_001053.4 linkuse as main transcriptc.156G>A p.Ala52= synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SSTR5ENST00000689027.1 linkuse as main transcriptc.156G>A p.Ala52= synonymous_variant 2/2 NM_001172560.3 P1
SSTR5ENST00000293897.7 linkuse as main transcriptc.156G>A p.Ala52= synonymous_variant 1/1 P1
SSTR5ENST00000711615.1 linkuse as main transcriptc.156G>A p.Ala52= synonymous_variant 2/2 P1
SSTR5ENST00000711616.1 linkuse as main transcriptc.156G>A p.Ala52= synonymous_variant 1/2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00216
AC:
329
AN:
152218
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000531
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000392
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.0197
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00125
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00257
AC:
609
AN:
237216
Hom.:
6
AF XY:
0.00241
AC XY:
311
AN XY:
129124
show subpopulations
Gnomad AFR exome
AF:
0.000606
Gnomad AMR exome
AF:
0.000600
Gnomad ASJ exome
AF:
0.000713
Gnomad EAS exome
AF:
0.000115
Gnomad SAS exome
AF:
0.000167
Gnomad FIN exome
AF:
0.0205
Gnomad NFE exome
AF:
0.00130
Gnomad OTH exome
AF:
0.00342
GnomAD4 exome
AF:
0.00163
AC:
2377
AN:
1454212
Hom.:
17
Cov.:
30
AF XY:
0.00157
AC XY:
1138
AN XY:
723132
show subpopulations
Gnomad4 AFR exome
AF:
0.000541
Gnomad4 AMR exome
AF:
0.000662
Gnomad4 ASJ exome
AF:
0.000461
Gnomad4 EAS exome
AF:
0.0000510
Gnomad4 SAS exome
AF:
0.000222
Gnomad4 FIN exome
AF:
0.0204
Gnomad4 NFE exome
AF:
0.00105
Gnomad4 OTH exome
AF:
0.00157
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00219
AC:
334
AN:
152336
Hom.:
5
Cov.:
33
AF XY:
0.00287
AC XY:
214
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.000529
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.0197
Gnomad4 NFE
AF:
0.00125
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00122
Hom.:
0
Bravo
AF:
0.000710
Asia WGS
AF:
0.00433
AC:
15
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

SSTR5-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 15, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
2.9
Dann
Benign
0.69

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.

Other links and lift over

dbSNP: rs4988485; hg19: chr16-1129024; API