rs28371667
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000574.5(CD55):c.980-159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 620,816 control chromosomes in the GnomAD database, including 98 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 0.014 ( 26 hom., cov: 32)
Exomes 𝑓: 0.016 ( 72 hom. )
Consequence
CD55
NM_000574.5 intron
NM_000574.5 intron
Scores
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.267
Genes affected
CD55 (HGNC:2665): (CD55 molecule (Cromer blood group)) This gene encodes a glycoprotein involved in the regulation of the complement cascade. Binding of the encoded protein to complement proteins accelerates their decay, thereby disrupting the cascade and preventing damage to host cells. Antigens present on this protein constitute the Cromer blood group system (CROM). Alternative splicing results in multiple transcript variants. The predominant transcript variant encodes a membrane-bound protein, but alternatively spliced transcripts may produce soluble proteins. [provided by RefSeq, Jul 2014]
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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 (MetaRNN=0.0038772523).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0135 (2062/152278) while in subpopulation NFE AF= 0.0201 (1366/68004). AF 95% confidence interval is 0.0192. There are 26 homozygotes in gnomad4. There are 953 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 26 BG,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD55 | NM_000574.5 | c.980-159C>T | intron_variant | ENST00000367064.9 | NP_000565.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD55 | ENST00000367064.9 | c.980-159C>T | intron_variant | 1 | NM_000574.5 | ENSP00000356031.4 |
Frequencies
GnomAD3 genomes AF: 0.0136 AC: 2062AN: 152160Hom.: 26 Cov.: 32
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GnomAD4 exome AF: 0.0162 AC: 7575AN: 468538Hom.: 72 Cov.: 5 AF XY: 0.0154 AC XY: 3838AN XY: 249108
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GnomAD4 genome AF: 0.0135 AC: 2062AN: 152278Hom.: 26 Cov.: 32 AF XY: 0.0128 AC XY: 953AN XY: 74460
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
Sift4G
Benign
T
Vest4
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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