chr1-207361901-C-A

Variant names:

• chr1-207361901-C-A
• rs1507765
• ENST00000695826.1:c.1082-10868C>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000695826.1	c.1082-10868C>A		intron_variant	Intron 9 of 9			ENSP00000512203.1
CD55	ENST00000618707.2	c.584-5469C>A		intron_variant	Intron 6 of 7	6		ENSP00000495477.1
CD55	ENST00000634386.1	n.166+22484C>A		intron_variant	Intron 3 of 4	5		ENSP00000493859.1

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

African (AFR) AF: 0.623 AC: 25830 AN: 41470

American (AMR) AF: 0.521 AC: 7959 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2137 AN: 5164

South Asian (SAS) AF: 0.535 AC: 2576 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5604 AN: 10570

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.536 AC: 36376 AN: 67914

Other (OTH) AF: 0.503 AC: 1062 AN: 2110

Alfa AF: 0.539 Hom.: 62595

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1507765; hg19: chr1-207535246;