dbSNP rs10746463: CD55:n.1027G>A (chr1-207337251-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 ENST00000465534.5(CD55):n.1027G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 932,012 control chromosomes in the GnomAD database, including 221,753 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 ( 36896 hom., cov: 32)

Exomes 𝑓: 0.68 ( 184857 hom. )

Consequence

CD55
ENST00000465534.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.51

Publications

20 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 (MetaRNN=0.0030991137).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD55	NM_000574.5 link	c.980-78G>A		intron_variant	Intron 7 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.980-78G>A		intron_variant	Intron 7 of 9	1	NM_000574.5	ENSP00000356031.4		P08174-1

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

105163

AN:

151934

Hom.:

36862

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.816

Gnomad AMR

AF:

0.696

Gnomad ASJ

AF:

0.860

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.753

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.732

GnomAD4 exome

AF:

0.684

AC:

533855

AN:

779960

Hom.:

184857

Cov.:

AF XY:

0.682

AC XY:

281202

AN XY:

412116

show subpopulations

African (AFR)

AF:

0.679

AC:

13473

AN:

19846

American (AMR)

AF:

0.669

AC:

25947

AN:

38778

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

17030

AN:

19810

East Asian (EAS)

AF:

0.506

AC:

18409

AN:

36406

South Asian (SAS)

AF:

0.594

AC:

41114

AN:

69160

European-Finnish (FIN)

AF:

0.747

AC:

38284

AN:

51266

Middle Eastern (MID)

AF:

0.810

AC:

3513

AN:

4338

European-Non Finnish (NFE)

AF:

0.696

AC:

349761

AN:

502752

Other (OTH)

AF:

0.700

AC:

26324

AN:

37604

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

8433

16867

25300

33734

42167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5112

10224

15336

20448

25560

<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:

105256

AN:

152052

Hom.:

36896

Cov.:

AF XY:

0.689

AC XY:

51201

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.684

AC:

28350

AN:

41444

American (AMR)

AF:

0.696

AC:

10635

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

2983

AN:

3470

East Asian (EAS)

AF:

0.425

AC:

2198

AN:

5172

South Asian (SAS)

AF:

0.573

AC:

2759

AN:

4812

European-Finnish (FIN)

AF:

0.753

AC:

7964

AN:

10582

Middle Eastern (MID)

AF:

0.833

AC:

245

AN:

294

European-Non Finnish (NFE)

AF:

0.704

AC:

47844

AN:

67982

Other (OTH)

AF:

0.731

AC:

1537

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1664

3328

4991

6655

8319

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:

0.663

Hom.:

5746

Bravo

AF:

0.689

TwinsUK

AF:

0.685

AC:

2541

ALSPAC

AF:

0.682

AC:

2629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.88

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.080

(source)

DANN

Benign

0.59

FATHMM_MKL

Benign

0.0031

LIST_S2

Benign

0.28

MetaRNN

Benign

0.0031

PhyloP100

-2.5

Sift4G

Benign

0.13

Vest4

0.10

MVP

0.57

GERP RS

-6.8

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