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GeneBe

16-1079189-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001172560.3(SSTR5):c.321C>T(p.Phe107=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,612,558 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0044 ( 16 hom. )

Consequence

SSTR5
NM_001172560.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.96
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 -9 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=-0.43).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-1079189-C-T is Benign according to our data. Variant chr16-1079189-C-T is described in ClinVar as [Benign]. Clinvar id is 771197.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=-1.96 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 582 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SSTR5NM_001172560.3 linkuse as main transcriptc.321C>T p.Phe107= synonymous_variant 2/2 ENST00000689027.1
SSTR5NM_001053.4 linkuse as main transcriptc.321C>T p.Phe107= synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SSTR5ENST00000689027.1 linkuse as main transcriptc.321C>T p.Phe107= synonymous_variant 2/2 NM_001172560.3 P1
SSTR5ENST00000293897.7 linkuse as main transcriptc.321C>T p.Phe107= synonymous_variant 1/1 P1
SSTR5ENST00000711615.1 linkuse as main transcriptc.321C>T p.Phe107= synonymous_variant 2/2 P1
SSTR5ENST00000711616.1 linkuse as main transcriptc.321C>T p.Phe107= synonymous_variant 1/2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00382
AC:
582
AN:
152246
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000651
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00791
Gnomad ASJ
AF:
0.00490
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00273
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00545
Gnomad OTH
AF:
0.00526
GnomAD3 exomes
AF:
0.00412
AC:
1028
AN:
249392
Hom.:
5
AF XY:
0.00418
AC XY:
567
AN XY:
135492
show subpopulations
Gnomad AFR exome
AF:
0.000560
Gnomad AMR exome
AF:
0.00440
Gnomad ASJ exome
AF:
0.00421
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.000752
Gnomad FIN exome
AF:
0.00409
Gnomad NFE exome
AF:
0.00599
Gnomad OTH exome
AF:
0.00657
GnomAD4 exome
AF:
0.00438
AC:
6401
AN:
1460194
Hom.:
16
Cov.:
30
AF XY:
0.00435
AC XY:
3163
AN XY:
726420
show subpopulations
Gnomad4 AFR exome
AF:
0.000627
Gnomad4 AMR exome
AF:
0.00472
Gnomad4 ASJ exome
AF:
0.00463
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.000835
Gnomad4 FIN exome
AF:
0.00443
Gnomad4 NFE exome
AF:
0.00486
Gnomad4 OTH exome
AF:
0.00490
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00382
AC:
582
AN:
152364
Hom.:
2
Cov.:
33
AF XY:
0.00365
AC XY:
272
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.000649
Gnomad4 AMR
AF:
0.00790
Gnomad4 ASJ
AF:
0.00490
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00273
Gnomad4 NFE
AF:
0.00545
Gnomad4 OTH
AF:
0.00521
Alfa
AF:
0.00234
Hom.:
0
Bravo
AF:
0.00442
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00649
EpiControl
AF:
0.00729

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
5.9
Dann
Benign
0.90

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: rs4988486; hg19: chr16-1129189; COSMIC: COSV99559659; COSMIC: COSV99559659; API