rs35109010

Positions:

• chr1-207362678-AATG-A
• chr1-207362678-AATG-AATGATG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000695826.1(CD55):​c.1082-10086_1082-10084del 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 0.49 (18396 hom., cov: 0)
• Consequence: CD55 ENST00000695826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD55	ENST00000618707.2	c.586-4687_586-4685del		intron_variant
CD55	ENST00000695826.1	c.1082-10086_1082-10084del		intron_variant				A2
CD55	ENST00000634386.1	c.168-22539_168-22537del		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74102 AN: 151524 Hom.: 18388 Cov.: 0

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.489 AC: 74126 AN: 151642 Hom.: 18396 Cov.: 0 AF XY: 0.491 AC XY: 36319 AN XY: 74036

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.457

Alfa AF: 0.509 Hom.: 2448

Bravo AF: 0.483

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35109010; hg19: chr1-207536023;