rs1507757

chr1-207331403-C-Achr1-207331403-C-T

Variant summary

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

The NM_000574.5(CD55):c.853+107C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 892,596 control chromosomes in the GnomAD database, including 215,146 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 0.69 (36881 hom., cov: 32)
  • Exomes 𝑓: 0.69 (178265 hom.)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD55	NM_000574.5	c.853+107C>A		intron_variant		ENST00000367064.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD55	ENST00000367064.9	c.853+107C>A		intron_variant		1	NM_000574.5	P2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105130 AN: 151882 Hom.: 36847 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.731

GnomAD4 exome AF: 0.691 AC: 511644 AN: 740596 Hom.: 178265 AF XY: 0.688 AC XY: 268932 AN XY: 390908

Gnomad4 AFR exome AF: 0.675

Gnomad4 AMR exome AF: 0.666

Gnomad4 ASJ exome AF: 0.859

Gnomad4 EAS exome AF: 0.508

Gnomad4 SAS exome AF: 0.591

Gnomad4 FIN exome AF: 0.744

Gnomad4 NFE exome AF: 0.704

Gnomad4 OTH exome AF: 0.705

GnomAD4 genome AF: 0.692 AC: 105223 AN: 152000 Hom.: 36881 Cov.: 32 AF XY: 0.689 AC XY: 51181 AN XY: 74292

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.730

Alfa AF: 0.638 Hom.: 2516

Bravo AF: 0.690

Asia WGS AF: 0.477 AC: 1662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.38
Dann	Benign	0.55

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: rs1507757; hg19: chr1-207504748;