rs12721503
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000457277.5(CFLAR):c.*139T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,271,616 control chromosomes in the GnomAD database, including 348 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 0.018 ( 58 hom., cov: 32)
Exomes 𝑓: 0.020 ( 290 hom. )
Consequence
CFLAR
ENST00000457277.5 3_prime_UTR
ENST00000457277.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.553
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=-0.87).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0179 (2722/152304) while in subpopulation SAS AF= 0.0267 (129/4828). AF 95% confidence interval is 0.023. There are 58 homozygotes in gnomad4. There are 1474 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2721 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFLAR | NM_003879.7 | c.1305-616T>C | intron_variant | ENST00000309955.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFLAR | ENST00000309955.8 | c.1305-616T>C | intron_variant | 1 | NM_003879.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2721AN: 152186Hom.: 58 Cov.: 32
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GnomAD4 exome AF: 0.0198 AC: 22160AN: 1119312Hom.: 290 Cov.: 14 AF XY: 0.0200 AC XY: 10846AN XY: 541396
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GnomAD4 genome ? AF: 0.0179 AC: 2722AN: 152304Hom.: 58 Cov.: 32 AF XY: 0.0198 AC XY: 1474AN XY: 74468
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3478
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