11-33725787-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000611.6(CD59):c.-18-3324G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,930 control chromosomes in the GnomAD database, including 28,721 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 0.61 (28721 hom., cov: 31)
• Consequence: CD59 NM_000611.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD59	NM_000611.6	c.-18-3324G>A		intron_variant		ENST00000642928.2
CD59	NM_203329.3	c.-18-3324G>A		intron_variant
CD59	NM_203330.2	c.-18-3324G>A		intron_variant
CD59	NM_203331.3	c.-18-3324G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD59	ENST00000642928.2	c.-18-3324G>A		intron_variant			NM_000611.6	P1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92999 AN: 151812 Hom.: 28683 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.616

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93083 AN: 151930 Hom.: 28721 Cov.: 31 AF XY: 0.608 AC XY: 45157 AN XY: 74228

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.620

Alfa AF: 0.606 Hom.: 34439

Bravo AF: 0.604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.95
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs861256; hg19: chr11-33747333;