rs28371626

chr1-207337515-G-A

Variant summary

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

The NM_000574.5(CD55):c.1060+106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0266 in 678,418 control chromosomes in the GnomAD database, including 378 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 0.023 (81 hom., cov: 32)
  • Exomes 𝑓: 0.028 (297 hom.)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

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=-0.75).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD55	NM_000574.5	c.1060+106G>A		intron_variant		ENST00000367064.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD55	ENST00000367064.9	c.1060+106G>A		intron_variant		1	NM_000574.5	P2

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3503 AN: 152064 Hom.: 81 Cov.: 32

Gnomad AFR AF: 0.00377

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0282

GnomAD4 exome AF: 0.0277 AC: 14553 AN: 526236 Hom.: 297 Cov.: 6 AF XY: 0.0276 AC XY: 7830 AN XY: 283764

Gnomad4 AFR exome AF: 0.00475

Gnomad4 AMR exome AF: 0.0165

Gnomad4 ASJ exome AF: 0.0542

Gnomad4 EAS exome AF: 0.0000935

Gnomad4 SAS exome AF: 0.0122

Gnomad4 FIN exome AF: 0.0628

Gnomad4 NFE exome AF: 0.0283

Gnomad4 OTH exome AF: 0.0277

GnomAD4 genome AF: 0.0230 AC: 3501 AN: 152182 Hom.: 81 Cov.: 32 AF XY: 0.0241 AC XY: 1791 AN XY: 74398

Gnomad4 AFR AF: 0.00376

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0652

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0275

Alfa AF: 0.0287 Hom.: 10

Bravo AF: 0.0186

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	9.3
Dann	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs28371626; hg19: chr1-207510860;