chr16-1078901-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001172560.3(SSTR5):c.33C>T(p.Ser11=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000605 in 1,606,248 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0033 ( 7 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 2 hom. )
Consequence
SSTR5
NM_001172560.3 synonymous
NM_001172560.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.92
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
Variant 16-1078901-C-T is Benign according to our data. Variant chr16-1078901-C-T is described in ClinVar as [Benign]. Clinvar id is 733020.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 490 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSTR5 | NM_001172560.3 | c.33C>T | p.Ser11= | synonymous_variant | 2/2 | ENST00000689027.1 | |
SSTR5 | NM_001053.4 | c.33C>T | p.Ser11= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSTR5 | ENST00000689027.1 | c.33C>T | p.Ser11= | synonymous_variant | 2/2 | NM_001172560.3 | P1 | ||
SSTR5 | ENST00000293897.7 | c.33C>T | p.Ser11= | synonymous_variant | 1/1 | P1 | |||
SSTR5 | ENST00000711615.1 | c.33C>T | p.Ser11= | synonymous_variant | 2/2 | P1 | |||
SSTR5 | ENST00000711616.1 | c.33C>T | p.Ser11= | synonymous_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.00322 AC: 490AN: 152202Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.000764 AC: 178AN: 232940Hom.: 1 AF XY: 0.000545 AC XY: 70AN XY: 128382
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GnomAD4 exome AF: 0.000327 AC: 476AN: 1453928Hom.: 2 Cov.: 29 AF XY: 0.000292 AC XY: 211AN XY: 723400
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 15, 2018 | - - |
SSTR5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This 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
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at