1-207362286-T-C

Variant names:

• chr1-207362286-T-C
• rs12066318
• ENST00000695826.1:c.1082-10483T>C

Variant summary

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

The ENST00000695826.1(CD55):​c.1082-10483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,062 control chromosomes in the GnomAD database, including 11,709 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 0.38 (11709 hom., cov: 31)
• Consequence: CD55 ENST00000695826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000695826.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	ENST00000695826.1		c.1082-10483T>C		intron	N/A	ENSP00000512203.1
	CD55	ENST00000618707.2	TSL:6	c.584-5084T>C		intron	N/A	ENSP00000495477.1
	CD55	ENST00000634386.1	TSL:5	n.166+22869T>C		intron	N/A	ENSP00000493859.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57396 AN: 151944 Hom.: 11695 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.378 AC: 57434 AN: 152062 Hom.: 11709 Cov.: 31 AF XY: 0.378 AC XY: 28115 AN XY: 74312

African (AFR) AF: 0.215 AC: 8910 AN: 41484

American (AMR) AF: 0.443 AC: 6764 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1907 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1848 AN: 4826

European-Finnish (FIN) AF: 0.451 AC: 4758 AN: 10544

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29916 AN: 67980

Other (OTH) AF: 0.438 AC: 922 AN: 2106

Alfa AF: 0.404 Hom.: 1619

Bravo AF: 0.373

Asia WGS AF: 0.329 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.63
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs12066318; hg19: chr1-207535631;