dbSNP rs2184476: CD55:c.853+28G>A (chr1-207331324-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000574.5(CD55):c.853+28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 1,588,398 control chromosomes in the GnomAD database, including 378,001 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 0.69 ( 36862 hom., cov: 31)

Exomes 𝑓: 0.69 ( 341139 hom. )

Consequence

CD55
NM_000574.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00100

Publications

13 publications found

Variant links:

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)

CD55 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_000574.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD55	NM_000574.5	MANE Select	c.853+28G>A	intron	N/A	NP_000565.1	P08174-1
CD55	NM_001300902.2		c.853+28G>A	intron	N/A	NP_001287831.1	B1AP13
CD55	NM_001114752.3		c.853+28G>A	intron	N/A	NP_001108224.1	P08174-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD55	ENST00000367064.9	TSL:1 MANE Select	c.853+28G>A	intron	N/A	ENSP00000356031.4	P08174-1
CD55	ENST00000367063.6	TSL:1	c.853+28G>A	intron	N/A	ENSP00000356030.2	B1AP13
CD55	ENST00000314754.12	TSL:1	c.853+28G>A	intron	N/A	ENSP00000316333.8	P08174-2

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

105093

AN:

151856

Hom.:

36828

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.815

Gnomad AMR

AF:

0.697

Gnomad ASJ

AF:

0.860

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.732

GnomAD2 exomes

AF:

0.669

AC:

164655

AN:

246148

AF XY:

0.670

show subpopulations

Gnomad AFR exome

AF:

0.680

Gnomad AMR exome

AF:

0.652

Gnomad ASJ exome

AF:

0.856

Gnomad EAS exome

AF:

0.404

Gnomad FIN exome

AF:

0.749

Gnomad NFE exome

AF:

0.702

Gnomad OTH exome

AF:

0.715

GnomAD4 exome

AF:

0.686

AC:

985817

AN:

1436424

Hom.:

341139

Cov.:

AF XY:

0.685

AC XY:

490563

AN XY:

715844

show subpopulations

African (AFR)

AF:

0.675

AC:

22079

AN:

32686

American (AMR)

AF:

0.662

AC:

28443

AN:

42952

Ashkenazi Jewish (ASJ)

AF:

0.857

AC:

22095

AN:

25780

East Asian (EAS)

AF:

0.498

AC:

19662

AN:

39494

South Asian (SAS)

AF:

0.591

AC:

49830

AN:

84374

European-Finnish (FIN)

AF:

0.746

AC:

39751

AN:

53264

Middle Eastern (MID)

AF:

0.807

AC:

4608

AN:

5708

European-Non Finnish (NFE)

AF:

0.694

AC:

758121

AN:

1092624

Other (OTH)

AF:

0.692

AC:

41228

AN:

59542

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

14611

29222

43832

58443

73054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19054

38108

57162

76216

95270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.692

AC:

105186

AN:

151974

Hom.:

36862

Cov.:

AF XY:

0.689

AC XY:

51137

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.684

AC:

28333

AN:

41440

American (AMR)

AF:

0.697

AC:

10637

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

2983

AN:

3470

East Asian (EAS)

AF:

0.425

AC:

2196

AN:

5172

South Asian (SAS)

AF:

0.574

AC:

2766

AN:

4822

European-Finnish (FIN)

AF:

0.751

AC:

7914

AN:

10538

Middle Eastern (MID)

AF:

0.833

AC:

245

AN:

294

European-Non Finnish (NFE)

AF:

0.704

AC:

47827

AN:

67944

Other (OTH)

AF:

0.731

AC:

1543

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1613

3226

4840

6453

8066

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

812

1624

2436

3248

4060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.694

Hom.:

4793

Bravo

AF:

0.693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

3.5

(source)

DANN

Benign

0.74

PhyloP100

-0.0010

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over