rs10538602

Variant names:

• chr11-33731325-CAT-C
• rs10538602
• NM_000611.6:c.-19+5055_-19+5056delAT

Your query was ambiguous. Multiple possible variants found:

• chr11-33731325-CAT-C
• chr11-33731325-CAT-CATAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000611.6(CD59):​c.-19+5055_-19+5056delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.28 (6327 hom., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: CD59 NM_000611.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• Publications: 0 publications found

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]

CD59 Gene-Disease associations (from GenCC):

• primary CD59 deficiency

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD59	NM_000611.6	c.-19+5055_-19+5056delAT		intron_variant	Intron 1 of 3	ENST00000642928.2	NP_000602.1
CD59	NM_203329.3	c.-19+2168_-19+2169delAT		intron_variant	Intron 2 of 4		NP_976074.1
CD59	NM_203330.2	c.-19+97_-19+98delAT		intron_variant	Intron 3 of 5		NP_976075.1
CD59	NM_203331.3	c.-19+97_-19+98delAT		intron_variant	Intron 2 of 4		NP_976076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD59	ENST00000642928.2	c.-19+5055_-19+5056delAT		intron_variant	Intron 1 of 3		NM_000611.6	ENSP00000494884.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43059 AN: 151328 Hom.: 6325 Cov.: 19

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.284 AC: 43069 AN: 151440 Hom.: 6327 Cov.: 19 AF XY: 0.283 AC XY: 20933 AN XY: 73960

African (AFR) AF: 0.212 AC: 8744 AN: 41232

American (AMR) AF: 0.312 AC: 4736 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1356 AN: 5162

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4814

European-Finnish (FIN) AF: 0.293 AC: 3057 AN: 10426

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21187 AN: 67830

Other (OTH) AF: 0.322 AC: 679 AN: 2106

Alfa AF: 0.158 Hom.: 307

Bravo AF: 0.284

Asia WGS AF: 0.273 AC: 949 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.87
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10538602; hg19: chr11-33752871;