rs11117564

Positions:

• chr1-207363626-A-C
• chr1-207363626-A-G
• chr1-207363626-A-T

Variant summary

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

The ENST00000695826.1(CD55):​c.1082-9143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,964 control chromosomes in the GnomAD database, including 18,294 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 0.49 (18294 hom., cov: 32)
• Consequence: CD55 ENST00000695826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000618707.2	c.586-3744A>C		intron_variant				ENSP00000495477
CD55	ENST00000695826.1	c.1082-9143A>C		intron_variant				ENSP00000512203	A2
CD55	ENST00000634386.1	c.168-21596A>C		intron_variant, NMD_transcript_variant		5		ENSP00000493859

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73781 AN: 151848 Hom.: 18285 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.486 AC: 73807 AN: 151964 Hom.: 18294 Cov.: 32 AF XY: 0.488 AC XY: 36247 AN XY: 74274

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.454

Alfa AF: 0.519 Hom.: 40387

Bravo AF: 0.478

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11117564; hg19: chr1-207536971;