rs925131

Variant names:

• chr1-207330376-G-A
• rs925131
• NM_000574.5:c.665-732G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-207330376-G-A
• chr1-207330376-G-C

Variant summary

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

The NM_000574.5(CD55):​c.665-732G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,318 control chromosomes in the GnomAD database, including 5,524 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 0.24 (5524 hom., cov: 31)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD55	NM_000574.5	c.665-732G>A		intron_variant	Intron 5 of 9	ENST00000367064.9	NP_000565.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000367064.9	c.665-732G>A		intron_variant	Intron 5 of 9	1	NM_000574.5	ENSP00000356031.4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35632 AN: 151232 Hom.: 5530 Cov.: 31

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.235 AC: 35627 AN: 151318 Hom.: 5524 Cov.: 31 AF XY: 0.241 AC XY: 17821 AN XY: 73852

African (AFR) AF: 0.0643 AC: 2653 AN: 41280

American (AMR) AF: 0.280 AC: 4246 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3466

East Asian (EAS) AF: 0.576 AC: 2955 AN: 5132

South Asian (SAS) AF: 0.423 AC: 2032 AN: 4802

European-Finnish (FIN) AF: 0.250 AC: 2565 AN: 10262

Middle Eastern (MID) AF: 0.156 AC: 45 AN: 288

European-Non Finnish (NFE) AF: 0.295 AC: 20044 AN: 67884

Other (OTH) AF: 0.220 AC: 463 AN: 2104

Alfa AF: 0.203 Hom.: 1739

Bravo AF: 0.228

Asia WGS AF: 0.497 AC: 1722 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs925131; hg19: chr1-207503721;