rs2518142
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003879.7(CFLAR):c.794-24G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 1,602,208 control chromosomes in the GnomAD database, including 638,173 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 0.88 ( 59435 hom., cov: 30)
Exomes 𝑓: 0.89 ( 578738 hom. )
Consequence
CFLAR
NM_003879.7 intron
NM_003879.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.13
Genes affected
CFLAR (HGNC:1876): (CASP8 and FADD like apoptosis regulator) The protein encoded by this gene is a regulator of apoptosis and is structurally similar to caspase-8. However, the encoded protein lacks caspase activity and appears to be itself cleaved into two peptides by caspase-8. Several transcript variants encoding different isoforms have been found for this gene, and partial evidence for several more variants exists. [provided by RefSeq, Feb 2011]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFLAR | NM_003879.7 | c.794-24G>A | intron_variant | ENST00000309955.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFLAR | ENST00000309955.8 | c.794-24G>A | intron_variant | 1 | NM_003879.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.882 AC: 134086AN: 151976Hom.: 59392 Cov.: 30
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GnomAD3 exomes AF: 0.870 AC: 213615AN: 245416Hom.: 93766 AF XY: 0.865 AC XY: 115027AN XY: 133008
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GnomAD4 exome AF: 0.891 AC: 1292656AN: 1450114Hom.: 578738 Cov.: 41 AF XY: 0.886 AC XY: 638864AN XY: 720878
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GnomAD4 genome ? AF: 0.882 AC: 134186AN: 152094Hom.: 59435 Cov.: 30 AF XY: 0.880 AC XY: 65410AN XY: 74362
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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