rs1466113
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001050.3(SSTR2):c.-92-49C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,054,650 control chromosomes in the GnomAD database, including 192,653 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.64 ( 31600 hom., cov: 33)
Exomes 𝑓: 0.60 ( 161053 hom. )
Consequence
SSTR2
NM_001050.3 intron
NM_001050.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.415
Genes affected
SSTR2 (HGNC:11331): (somatostatin receptor 2) Somatostatin acts at many sites to inhibit the release of many hormones and other secretory proteins. The biologic effects of somatostatin are probably mediated by a family of G protein-coupled receptors that are expressed in a tissue-specific manner. SSTR2 is a member of the superfamily of receptors having seven transmembrane segments and is expressed in highest levels in cerebrum and kidney. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSTR2 | NM_001050.3 | c.-92-49C>G | intron_variant | ENST00000357585.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSTR2 | ENST00000357585.4 | c.-92-49C>G | intron_variant | 1 | NM_001050.3 | P1 | |||
SSTR2 | ENST00000579323.5 | n.447-49C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.640 AC: 97218AN: 151990Hom.: 31557 Cov.: 33
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GnomAD4 exome AF: 0.595 AC: 537448AN: 902542Hom.: 161053 Cov.: 12 AF XY: 0.599 AC XY: 269261AN XY: 449618
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GnomAD4 genome ? AF: 0.640 AC: 97306AN: 152108Hom.: 31600 Cov.: 33 AF XY: 0.639 AC XY: 47529AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
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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