rs3795391
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002964.5(S100A8):c.-22-72A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,560,056 control chromosomes in the GnomAD database, including 9,360 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 0.084 ( 619 hom., cov: 32)
Exomes 𝑓: 0.11 ( 8741 hom. )
Consequence
S100A8
NM_002964.5 intron
NM_002964.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.14
Genes affected
S100A8 (HGNC:10498): (S100 calcium binding protein A8) 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. This protein may function in the inhibition of casein kinase and as a cytokine. Altered expression of this protein is associated with the disease cystic fibrosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
S100A8 | NM_002964.5 | c.-22-72A>G | intron_variant | ENST00000368733.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S100A8 | ENST00000368733.4 | c.-22-72A>G | intron_variant | 1 | NM_002964.5 | P1 | |||
S100A8 | ENST00000477801.1 | n.443A>G | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
S100A8 | ENST00000368732.5 | c.-22-72A>G | intron_variant | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0838 AC: 12748AN: 152098Hom.: 619 Cov.: 32
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GnomAD4 exome AF: 0.110 AC: 154537AN: 1407840Hom.: 8741 Cov.: 25 AF XY: 0.110 AC XY: 76792AN XY: 697284
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GnomAD4 genome ? AF: 0.0838 AC: 12752AN: 152216Hom.: 619 Cov.: 32 AF XY: 0.0831 AC XY: 6186AN XY: 74416
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at