rs11120766

Variant names:

• chr1-207361334-G-A
• rs11120766
• ENST00000945373.1:c.*33-1317G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-207361334-G-A
• chr1-207361334-G-C
• chr1-207361334-G-T

Variant summary

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

The ENST00000945373.1(CD55):​c.*33-1317G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,972 control chromosomes in the GnomAD database, including 18,578 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 (18578 hom., cov: 32)
• Consequence: CD55 ENST00000945373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• 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=-0.91).
• 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.*33-1317G>A		intron	N/A	ENSP00000615432.1
	CD55	ENST00000695826.1		c.1082-11435G>A		intron	N/A	ENSP00000512203.1
	CD55	ENST00000618707.2	TSL:6	c.584-6036G>A		intron	N/A	ENSP00000495477.1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74491 AN: 151854 Hom.: 18570 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.490 AC: 74515 AN: 151972 Hom.: 18578 Cov.: 32 AF XY: 0.492 AC XY: 36577 AN XY: 74290

African (AFR) AF: 0.414 AC: 17157 AN: 41440

American (AMR) AF: 0.498 AC: 7605 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1642 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2147 AN: 5168

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4820

European-Finnish (FIN) AF: 0.530 AC: 5599 AN: 10558

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36269 AN: 67940

Other (OTH) AF: 0.458 AC: 966 AN: 2110

Alfa AF: 0.489 Hom.: 5804

Bravo AF: 0.483

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.57
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs11120766; hg19: chr1-207534679;