rs642249
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001172560.3(SSTR5):āc.1044A>Gā(p.Pro348=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 1,606,566 control chromosomes in the GnomAD database, including 747,450 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: š 0.96 ( 69747 hom., cov: 36)
Exomes š: 0.96 ( 677703 hom. )
Consequence
SSTR5
NM_001172560.3 synonymous
NM_001172560.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.177
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=-0.89).
BP6
?
Variant 16-1079912-A-G is Benign according to our data. Variant chr16-1079912-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.177 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSTR5 | NM_001172560.3 | c.1044A>G | p.Pro348= | synonymous_variant | 2/2 | ENST00000689027.1 | |
SSTR5 | NM_001053.4 | c.1044A>G | p.Pro348= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSTR5 | ENST00000689027.1 | c.1044A>G | p.Pro348= | synonymous_variant | 2/2 | NM_001172560.3 | P1 | ||
SSTR5 | ENST00000293897.7 | c.1044A>G | p.Pro348= | synonymous_variant | 1/1 | P1 | |||
SSTR5 | ENST00000711615.1 | c.1044A>G | p.Pro348= | synonymous_variant | 2/2 | P1 | |||
SSTR5 | ENST00000711616.1 | c.*118A>G | 3_prime_UTR_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.957 AC: 145614AN: 152216Hom.: 69705 Cov.: 36
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GnomAD3 exomes AF: 0.956 AC: 226852AN: 237238Hom.: 108661 AF XY: 0.953 AC XY: 123591AN XY: 129734
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GnomAD4 exome AF: 0.965 AC: 1403240AN: 1454232Hom.: 677703 Cov.: 76 AF XY: 0.962 AC XY: 695749AN XY: 723110
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GnomAD4 genome ? AF: 0.957 AC: 145709AN: 152334Hom.: 69747 Cov.: 36 AF XY: 0.956 AC XY: 71183AN XY: 74480
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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