rs41275166
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000415002.7(CD59):c.-263A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 1,292,598 control chromosomes in the GnomAD database, including 328 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 0.015 ( 35 hom., cov: 32)
Exomes 𝑓: 0.020 ( 293 hom. )
Consequence
CD59
ENST00000415002.7 5_prime_UTR
ENST00000415002.7 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.17
Genes affected
CD59 (HGNC:1689): (CD59 molecule (CD59 blood group)) This gene encodes a cell surface glycoprotein that regulates complement-mediated cell lysis, and it is involved in lymphocyte signal transduction. This protein is a potent inhibitor of the complement membrane attack complex, whereby it binds complement C8 and/or C9 during the assembly of this complex, thereby inhibiting the incorporation of multiple copies of C9 into the complex, which is necessary for osmolytic pore formation. This protein also plays a role in signal transduction pathways in the activation of T cells. Mutations in this gene cause CD59 deficiency, a disease resulting in hemolytic anemia and thrombosis, and which causes cerebral infarction. Multiple alternatively spliced transcript variants, which encode the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]
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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).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0152 (2311/152280) while in subpopulation NFE AF= 0.0233 (1582/68010). AF 95% confidence interval is 0.0223. There are 35 homozygotes in gnomad4. There are 1100 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 35 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD59 | NM_000611.6 | c.-18-245A>G | intron_variant | ENST00000642928.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD59 | ENST00000642928.2 | c.-18-245A>G | intron_variant | NM_000611.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0152 AC: 2311AN: 152162Hom.: 35 Cov.: 32
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GnomAD4 exome AF: 0.0204 AC: 23297AN: 1140318Hom.: 293 Cov.: 26 AF XY: 0.0201 AC XY: 11035AN XY: 549686
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GnomAD4 genome ? AF: 0.0152 AC: 2311AN: 152280Hom.: 35 Cov.: 32 AF XY: 0.0148 AC XY: 1100AN XY: 74466
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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