1-207363500-T-G

Variant names:

• chr1-207363500-T-G
• rs11120769
• ENST00000945373.1:c.*882T>G

Variant summary

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

The ENST00000945373.1(CD55):​c.*882T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,982 control chromosomes in the GnomAD database, including 18,313 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 0.49 (18313 hom., cov: 32)
• Consequence: CD55 ENST00000945373.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000945373.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	ENST00000945373.1		c.*882T>G		3_prime_UTR	Exon 11 of 11	ENSP00000615432.1
	CD55	ENST00000695826.1		c.1082-9269T>G		intron	N/A	ENSP00000512203.1
	CD55	ENST00000618707.2	TSL:6	c.584-3870T>G		intron	N/A	ENSP00000495477.1

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73833 AN: 151862 Hom.: 18304 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.486 AC: 73859 AN: 151982 Hom.: 18313 Cov.: 32 AF XY: 0.488 AC XY: 36271 AN XY: 74276

African (AFR) AF: 0.399 AC: 16555 AN: 41452

American (AMR) AF: 0.496 AC: 7578 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1605 AN: 3462

East Asian (EAS) AF: 0.416 AC: 2148 AN: 5164

South Asian (SAS) AF: 0.535 AC: 2583 AN: 4824

European-Finnish (FIN) AF: 0.530 AC: 5588 AN: 10544

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

European-Non Finnish (NFE) AF: 0.534 AC: 36289 AN: 67954

Other (OTH) AF: 0.454 AC: 960 AN: 2116

Alfa AF: 0.503 Hom.: 6816

Bravo AF: 0.478

Asia WGS AF: 0.477 AC: 1657 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	2.1
DANN	Benign	0.42
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11120769; hg19: chr1-207536845;