NM_000574.5:c.854-1546A>G

Variant names:

• chr1-207335147-A-G
• rs1354942
• NM_000574.5:c.854-1546A>G

Variant summary

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

The NM_000574.5(CD55):​c.854-1546A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 150,908 control chromosomes in the GnomAD database, including 6,187 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 0.27 (6187 hom., cov: 32)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 10 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: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000574.5. 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
	CD55	NM_000574.5	MANE Select	c.854-1546A>G		intron	N/A	NP_000565.1	P08174-1
	CD55	NM_001300902.2		c.854-1546A>G		intron	N/A	NP_001287831.1	B1AP13
	CD55	NM_001114752.3		c.854-1546A>G		intron	N/A	NP_001108224.1	P08174-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	ENST00000367064.9	TSL:1 MANE Select	c.854-1546A>G		intron	N/A	ENSP00000356031.4	P08174-1
	CD55	ENST00000367063.6	TSL:1	c.854-1546A>G		intron	N/A	ENSP00000356030.2	B1AP13
	CD55	ENST00000314754.12	TSL:1	c.854-1546A>G		intron	N/A	ENSP00000316333.8	P08174-2

Frequencies

GnomAD3 genomes AF: 0.271 AC: 40909 AN: 150790 Hom.: 6191 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.271 AC: 40924 AN: 150908 Hom.: 6187 Cov.: 32 AF XY: 0.276 AC XY: 20326 AN XY: 73730

African (AFR) AF: 0.185 AC: 7554 AN: 40850

American (AMR) AF: 0.293 AC: 4442 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 488 AN: 3448

East Asian (EAS) AF: 0.574 AC: 2967 AN: 5166

South Asian (SAS) AF: 0.426 AC: 2033 AN: 4772

European-Finnish (FIN) AF: 0.250 AC: 2608 AN: 10444

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20097 AN: 67768

Other (OTH) AF: 0.248 AC: 520 AN: 2098

Alfa AF: 0.290 Hom.: 11019

Bravo AF: 0.267

Asia WGS AF: 0.507 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.2
DANN	Benign	0.92
PhyloP100		0.28
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: rs1354942; hg19: chr1-207508492;