rs35109010

Variant names:

• chr1-207362678-AATG-A
• rs35109010
• ENST00000695826.1:c.1082-10090_1082-10088delATG

Your query was ambiguous. Multiple possible variants found:

• chr1-207362678-AATG-A
• chr1-207362678-AATG-AATGATG

Variant summary

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

The ENST00000695826.1(CD55):​c.1082-10090_1082-10088delATG 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 0.49 (18396 hom., cov: 0)
• Consequence: CD55 ENST00000695826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.529 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.1082-10090_1082-10088delATG		intron_variant	Intron 9 of 9			ENSP00000512203.1
CD55	ENST00000618707.2	c.584-4691_584-4689delATG		intron_variant	Intron 6 of 7	6		ENSP00000495477.1
CD55	ENST00000634386.1	n.167-22543_167-22541delATG		intron_variant	Intron 3 of 4	5		ENSP00000493859.1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74102 AN: 151524 Hom.: 18388 Cov.: 0

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.489 AC: 74126 AN: 151642 Hom.: 18396 Cov.: 0 AF XY: 0.491 AC XY: 36319 AN XY: 74036

African (AFR) AF: 0.413 AC: 17068 AN: 41342

American (AMR) AF: 0.497 AC: 7574 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2127 AN: 5152

South Asian (SAS) AF: 0.533 AC: 2561 AN: 4802

European-Finnish (FIN) AF: 0.525 AC: 5486 AN: 10454

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36183 AN: 67868

Other (OTH) AF: 0.457 AC: 966 AN: 2112

Alfa AF: 0.509 Hom.: 2448

Bravo AF: 0.483

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs35109010; hg19: chr1-207536023;