rs1507765

Positions:

• chr1-207361901-C-A

Variant summary

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

The ENST00000695826.1(CD55):​c.1082-10868C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,974 control chromosomes in the GnomAD database, including 23,313 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 0.55 (23313 hom., cov: 31)
• Consequence: CD55 ENST00000695826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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.586-5469C>A		intron_variant				ENSP00000495477
CD55	ENST00000695826.1	c.1082-10868C>A		intron_variant				ENSP00000512203	A2
CD55	ENST00000634386.1	c.167+22484C>A		intron_variant, NMD_transcript_variant		5		ENSP00000493859

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83701 AN: 151858 Hom.: 23289 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.551 AC: 83762 AN: 151974 Hom.: 23313 Cov.: 31 AF XY: 0.551 AC XY: 40960 AN XY: 74292

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.503

Alfa AF: 0.531 Hom.: 27684

Bravo AF: 0.552

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.62
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1507765; hg19: chr1-207535246;