rs2186358
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000397648.1(S100B):c.-47G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 1,586,718 control chromosomes in the GnomAD database, including 487,182 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 0.76 ( 44033 hom., cov: 32)
Exomes 𝑓: 0.78 ( 443149 hom. )
Consequence
S100B
ENST00000397648.1 5_prime_UTR
ENST00000397648.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.56
Genes affected
S100B (HGNC:10500): (S100 calcium binding protein B) The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21; however, this gene is located at 21q22.3. This protein may function in Neurite extension, proliferation of melanoma cells, stimulation of Ca2+ fluxes, inhibition of PKC-mediated phosphorylation, astrocytosis and axonal proliferation, and inhibition of microtubule assembly. Chromosomal rearrangements and altered expression of this gene have been implicated in several neurological, neoplastic, and other types of diseases, including Alzheimer's disease, Down's syndrome, epilepsy, amyotrophic lateral sclerosis, melanoma, and type I diabetes. [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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
S100B | NM_006272.3 | c.-1-46G>T | intron_variant | ENST00000291700.9 | |||
S100B | XM_017028424.3 | c.-8-39G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S100B | ENST00000397648.1 | c.-47G>T | 5_prime_UTR_variant | 1/2 | 1 | P1 | |||
S100B | ENST00000291700.9 | c.-1-46G>T | intron_variant | 1 | NM_006272.3 | P1 | |||
S100B | ENST00000367071.4 | c.-1-46G>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.757 AC: 115008AN: 151974Hom.: 44008 Cov.: 32
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GnomAD3 exomes AF: 0.793 AC: 185045AN: 233228Hom.: 73792 AF XY: 0.796 AC XY: 100492AN XY: 126286
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GnomAD4 exome AF: 0.785 AC: 1126057AN: 1434624Hom.: 443149 Cov.: 26 AF XY: 0.786 AC XY: 561578AN XY: 714060
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GnomAD4 genome ? AF: 0.757 AC: 115087AN: 152094Hom.: 44033 Cov.: 32 AF XY: 0.764 AC XY: 56773AN XY: 74344
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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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Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -13
Find out detailed SpliceAI scores and Pangolin per-transcript scores at