chr1-207361981-TA-T

Variant names:

• chr1-207361981-TA-T
• rs11307618
• ENST00000695826.1:c.1082-10787delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000695826.1(CD55):​c.1082-10787delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11525 hom., cov: 0)
• Consequence: CD55 ENST00000695826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 1 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.434 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.1082-10787delA		intron_variant	Intron 9 of 9			ENSP00000512203.1
CD55	ENST00000618707.2	c.584-5388delA		intron_variant	Intron 6 of 7	6		ENSP00000495477.1
CD55	ENST00000634386.1	n.166+22565delA		intron_variant	Intron 3 of 4	5		ENSP00000493859.1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57054 AN: 151548 Hom.: 11511 Cov.: 0

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.376 AC: 57092 AN: 151666 Hom.: 11525 Cov.: 0 AF XY: 0.377 AC XY: 27904 AN XY: 74082

African (AFR) AF: 0.216 AC: 8944 AN: 41466

American (AMR) AF: 0.441 AC: 6712 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1875 AN: 5138

South Asian (SAS) AF: 0.383 AC: 1840 AN: 4810

European-Finnish (FIN) AF: 0.447 AC: 4680 AN: 10474

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

European-Non Finnish (NFE) AF: 0.439 AC: 29725 AN: 67780

Other (OTH) AF: 0.436 AC: 920 AN: 2108

Alfa AF: 0.403 Hom.: 1574

Bravo AF: 0.373

Asia WGS AF: 0.327 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs11307618; hg19: chr1-207535326;