dbSNP rs1507757: CD55:c.853+107C>A (chr1-207331403-C-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+107C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 892,596 control chromosomes in the GnomAD database, including 215,146 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 ( 36881 hom., cov: 32)

Exomes 𝑓: 0.69 ( 178265 hom. )

Consequence

CD55
NM_000574.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.737

Publications

10 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: Labcorp Genetics (formerly Invitae), Orphanet

CD55 links:

Genome browser will be placed here

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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD55	NM_000574.5 link	c.853+107C>A		intron_variant	Intron 6 of 9	ENST00000367064.9	NP_000565.1	P08174-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000367064.9 link	c.853+107C>A		intron_variant	Intron 6 of 9	1	NM_000574.5	ENSP00000356031.4		P08174-1

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

105130

AN:

151882

Hom.:

36847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.813

Gnomad AMR

AF:

0.696

Gnomad ASJ

AF:

0.860

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.731

GnomAD4 exome

AF:

0.691

AC:

511644

AN:

740596

Hom.:

178265

AF XY:

0.688

AC XY:

268932

AN XY:

390908

show subpopulations

African (AFR)

AF:

0.675

AC:

11462

AN:

16974

American (AMR)

AF:

0.666

AC:

16950

AN:

25468

Ashkenazi Jewish (ASJ)

AF:

0.859

AC:

16329

AN:

19008

East Asian (EAS)

AF:

0.508

AC:

17204

AN:

33890

South Asian (SAS)

AF:

0.591

AC:

35919

AN:

60752

European-Finnish (FIN)

AF:

0.744

AC:

31543

AN:

42400

Middle Eastern (MID)

AF:

0.810

AC:

3107

AN:

3836

European-Non Finnish (NFE)

AF:

0.704

AC:

353668

AN:

502132

Other (OTH)

AF:

0.705

AC:

25462

AN:

36136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

7637

15274

22911

30548

38185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5440

10880

16320

21760

27200

<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:

105223

AN:

152000

Hom.:

36881

Cov.:

AF XY:

0.689

AC XY:

51181

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.684

AC:

28334

AN:

41408

American (AMR)

AF:

0.696

AC:

10642

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

2982

AN:

3468

East Asian (EAS)

AF:

0.425

AC:

2203

AN:

5184

South Asian (SAS)

AF:

0.573

AC:

2770

AN:

4830

European-Finnish (FIN)

AF:

0.751

AC:

7931

AN:

10556

Middle Eastern (MID)

AF:

0.833

AC:

245

AN:

294

European-Non Finnish (NFE)

AF:

0.704

AC:

47839

AN:

67956

Other (OTH)

AF:

0.730

AC:

1539

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1647

3294

4942

6589

8236

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:

0.675

Hom.:

11159

Bravo

AF:

0.690

Asia WGS

AF:

0.477

AC:

1662

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.38

(source)

DANN

Benign

0.55

PhyloP100

-0.74

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over