rs7544288

Variant names:

• chr1-207335677-G-A
• rs7544288
• NM_000574.5:c.854-1016G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-207335677-G-A
• chr1-207335677-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.854-1016G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,828 control chromosomes in the GnomAD database, including 11,712 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 0.38 (11712 hom., cov: 31)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD55	NM_000574.5	c.854-1016G>A		intron_variant	Intron 6 of 9	ENST00000367064.9	NP_000565.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000367064.9	c.854-1016G>A		intron_variant	Intron 6 of 9	1	NM_000574.5	ENSP00000356031.4

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57355 AN: 151710 Hom.: 11698 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.378 AC: 57393 AN: 151828 Hom.: 11712 Cov.: 31 AF XY: 0.379 AC XY: 28103 AN XY: 74176

African (AFR) AF: 0.215 AC: 8888 AN: 41408

American (AMR) AF: 0.443 AC: 6757 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1769 AN: 3462

East Asian (EAS) AF: 0.369 AC: 1901 AN: 5156

South Asian (SAS) AF: 0.392 AC: 1885 AN: 4814

European-Finnish (FIN) AF: 0.451 AC: 4746 AN: 10526

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

European-Non Finnish (NFE) AF: 0.440 AC: 29891 AN: 67890

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.419 Hom.: 53437

Bravo AF: 0.373

Asia WGS AF: 0.332 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.71
DANN	Benign	0.73
PhyloP100		-1.4
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: rs7544288; hg19: chr1-207509022;