rs4988514
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001048.4(SST):c.*22A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0948 in 1,612,634 control chromosomes in the GnomAD database, including 7,878 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 0.12 ( 1096 hom., cov: 32)
Exomes 𝑓: 0.093 ( 6782 hom. )
Consequence
SST
NM_001048.4 3_prime_UTR
NM_001048.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.653
Genes affected
SST (HGNC:11329): (somatostatin) The hormone somatostatin has active 14 aa and 28 aa forms that are produced by alternate cleavage of the single preproprotein encoded by this gene. Somatostatin is expressed throughout the body and inhibits the release of numerous secondary hormones by binding to high-affinity G-protein-coupled somatostatin receptors. This hormone is an important regulator of the endocrine system through its interactions with pituitary growth hormone, thyroid stimulating hormone, and most hormones of the gastrointestinal tract. Somatostatin also affects rates of neurotransmission in the central nervous system and proliferation of both normal and tumorigenic cells. [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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SST | NM_001048.4 | c.*22A>G | 3_prime_UTR_variant | 2/2 | ENST00000287641.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SST | ENST00000287641.4 | c.*22A>G | 3_prime_UTR_variant | 2/2 | 1 | NM_001048.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.116 AC: 17661AN: 151908Hom.: 1095 Cov.: 32
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GnomAD3 exomes AF: 0.109 AC: 27506AN: 251394Hom.: 1744 AF XY: 0.104 AC XY: 14186AN XY: 135878
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GnomAD4 exome AF: 0.0925 AC: 135153AN: 1460608Hom.: 6782 Cov.: 30 AF XY: 0.0919 AC XY: 66759AN XY: 726710
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GnomAD4 genome ? AF: 0.116 AC: 17670AN: 152026Hom.: 1096 Cov.: 32 AF XY: 0.119 AC XY: 8841AN XY: 74294
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at