rs1354942

chr1-207335147-A-Gchr1-207335147-A-T

Variant summary

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

The NM_000574.5(CD55):c.854-1546A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 150,908 control chromosomes in the GnomAD database, including 6,187 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 0.27 (6187 hom., cov: 32)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD55	NM_000574.5	c.854-1546A>G		intron_variant		ENST00000367064.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD55	ENST00000367064.9	c.854-1546A>G		intron_variant		1	NM_000574.5	P2

Frequencies

GnomAD3 genomes AF: 0.271 AC: 40909 AN: 150790 Hom.: 6191 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.271 AC: 40924 AN: 150908 Hom.: 6187 Cov.: 32 AF XY: 0.276 AC XY: 20326 AN XY: 73730

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.248

Alfa AF: 0.269 Hom.: 879

Bravo AF: 0.267

Asia WGS AF: 0.507 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	5.2
Dann	Benign	0.92

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: rs1354942; hg19: chr1-207508492;