rs77749396
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001165958.2(GSDMB):c.-14-257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000057 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
GSDMB
NM_001165958.2 intron
NM_001165958.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Genes affected
GSDMB (HGNC:23690): (gasdermin B) This gene encodes a member of the gasdermin-domain containing protein family. Other gasdermin-family genes are implicated in the regulation of apoptosis in epithelial cells, and are linked to cancer. Alternative splicing and the use of alternative promoters results in multiple transcript variants. Additional variants have been described, but they are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to be protein-coding. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSDMB | NM_001165958.2 | c.-14-257C>T | intron_variant | ENST00000418519.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSDMB | ENST00000418519.6 | c.-14-257C>T | intron_variant | 5 | NM_001165958.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000569 AC: 2AN: 35140Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000133 AC: 9AN: 67430Hom.: 0 Cov.: 0 AF XY: 0.000113 AC XY: 4AN XY: 35262
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GnomAD4 genome ? AF: 0.0000569 AC: 2AN: 35140Hom.: 0 Cov.: 0 AF XY: 0.0000580 AC XY: 1AN XY: 17246
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at