rs4844592

Variant names:

• chr1-207327866-T-A
• rs4844592
• NM_000574.5:c.664+1029T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-207327866-T-A
• chr1-207327866-T-C
• chr1-207327866-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000367064.9(CD55):​c.664+1029T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,970 control chromosomes in the GnomAD database, including 37,900 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 0.70 (37900 hom., cov: 31)
• Consequence: CD55 ENST00000367064.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 12 publications found

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]

CD55 Gene-Disease associations (from GenCC):

• protein-losing enteropathy

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000367064.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	NM_000574.5	MANE Select	c.664+1029T>A		intron	N/A	NP_000565.1
	CD55	NM_001300902.2		c.664+1029T>A		intron	N/A	NP_001287831.1
	CD55	NM_001114752.3		c.664+1029T>A		intron	N/A	NP_001108224.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	ENST00000367064.9	TSL:1 MANE Select	c.664+1029T>A		intron	N/A	ENSP00000356031.4
	CD55	ENST00000367063.6	TSL:1	c.664+1029T>A		intron	N/A	ENSP00000356030.2
	CD55	ENST00000314754.12	TSL:1	c.664+1029T>A		intron	N/A	ENSP00000316333.8

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106565 AN: 151852 Hom.: 37865 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.702 AC: 106661 AN: 151970 Hom.: 37900 Cov.: 31 AF XY: 0.698 AC XY: 51823 AN XY: 74252

African (AFR) AF: 0.718 AC: 29741 AN: 41430

American (AMR) AF: 0.698 AC: 10667 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2983 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2196 AN: 5164

South Asian (SAS) AF: 0.575 AC: 2766 AN: 4810

European-Finnish (FIN) AF: 0.751 AC: 7917 AN: 10538

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47848 AN: 67968

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.704 Hom.: 4444

Bravo AF: 0.700

Asia WGS AF: 0.476 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.50
DANN	Benign	0.56
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4844592; hg19: chr1-207501211;