dbSNP rs28371583: ENSG00000296591:n.116+352T>C (chr1-207321334-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000740658.1(ENSG00000296591):n.116+352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 159,474 control chromosomes in the GnomAD database, including 7,406 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 0.30 ( 7165 hom., cov: 33)

Exomes 𝑓: 0.24 ( 241 hom. )

Consequence

ENSG00000296591
ENST00000740658.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.614

Publications

9 publications found

Variant links:

Genes affected

ENSG00000296591 (HGNC:):

ENSG00000296591 links:

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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985251	XR_007066837.1 link	n.444+352T>C		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1 link	n.444+352T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000296591	ENST00000740658.1 link	n.116+352T>C	intron_variant	Intron 1 of 2
ENSG00000296591	ENST00000740659.1 link	n.96+352T>C	intron_variant	Intron 1 of 4
ENSG00000296591	ENST00000740660.1 link	n.89+352T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

45008

AN:

152008

Hom.:

7158

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.0552

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.238

AC:

1752

AN:

7348

Hom.:

241

Cov.:

AF XY:

0.230

AC XY:

878

AN XY:

3816

show subpopulations

African (AFR)

AF:

0.418

AC:

118

AN:

282

American (AMR)

AF:

0.195

AC:

AN:

154

Ashkenazi Jewish (ASJ)

AF:

0.366

AC:

104

AN:

284

East Asian (EAS)

AF:

0.0565

AC:

AN:

354

South Asian (SAS)

AF:

0.192

AC:

158

AN:

822

European-Finnish (FIN)

AF:

0.267

AC:

AN:

352

Middle Eastern (MID)

AF:

0.214

AC:

AN:

European-Non Finnish (NFE)

AF:

0.240

AC:

1101

AN:

4586

Other (OTH)

AF:

0.250

AC:

118

AN:

472

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

130

194

259

324

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.296

AC:

45052

AN:

152126

Hom.:

7165

Cov.:

AF XY:

0.293

AC XY:

21767

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.413

AC:

17137

AN:

41502

American (AMR)

AF:

0.240

AC:

3671

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1196

AN:

3472

East Asian (EAS)

AF:

0.0555

AC:

287

AN:

5170

South Asian (SAS)

AF:

0.181

AC:

875

AN:

4826

European-Finnish (FIN)

AF:

0.301

AC:

3178

AN:

10562

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17779

AN:

67978

Other (OTH)

AF:

0.276

AC:

582

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1631

3262

4894

6525

8156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.305

Hom.:

1206

Bravo

AF:

0.296

Asia WGS

AF:

0.138

AC:

482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.3

(source)

DANN

Benign

0.34

PhyloP100

-0.61

PromoterAI

-0.042

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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