rs5030551
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001226.4(CASP6):c.84-126C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 1,047,886 control chromosomes in the GnomAD database, including 249 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 0.025 ( 172 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 77 hom. )
Consequence
CASP6
NM_001226.4 intron
NM_001226.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.850
Genes affected
CASP6 (HGNC:1507): (caspase 6) This gene encodes a member of the cysteine-aspartic acid protease (caspase) family of enzymes. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic acid residues to produce two subunits, large and small, that dimerize to form the active enzyme. This protein is processed by caspases 7, 8 and 10, and is thought to function as a downstream enzyme in the caspase activation cascade. Alternative splicing of this gene results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Oct 2015]
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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=-0.76).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0856 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASP6 | NM_001226.4 | c.84-126C>T | intron_variant | ENST00000265164.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP6 | ENST00000265164.7 | c.84-126C>T | intron_variant | 1 | NM_001226.4 | P1 | |||
CASP6 | ENST00000352981.7 | c.41-3194C>T | intron_variant | 1 | |||||
CASP6 | ENST00000503684.5 | c.30-126C>T | intron_variant | 3 | |||||
CASP6 | ENST00000505486.1 | c.84-126C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0250 AC: 3807AN: 152146Hom.: 172 Cov.: 32
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GnomAD4 exome AF: 0.00261 AC: 2338AN: 895622Hom.: 77 AF XY: 0.00235 AC XY: 1064AN XY: 452902
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GnomAD4 genome ? AF: 0.0251 AC: 3817AN: 152264Hom.: 172 Cov.: 32 AF XY: 0.0233 AC XY: 1736AN XY: 74456
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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