1-207321780-G-A

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_000574.5(CD55):​c.15G>A​(p.Arg5Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000731 in 1,367,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 7.3e-7 ( 0 hom. )

Consequence

CD55
NM_000574.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.10

Publications

0 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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 1-207321780-G-A is Benign according to our data. Variant chr1-207321780-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2738078.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.1 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD55NM_000574.5 linkc.15G>A p.Arg5Arg synonymous_variant Exon 1 of 10 ENST00000367064.9 NP_000565.1 P08174-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD55ENST00000367064.9 linkc.15G>A p.Arg5Arg synonymous_variant Exon 1 of 10 1 NM_000574.5 ENSP00000356031.4 P08174-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.31e-7
AC:
1
AN:
1367678
Hom.:
0
Cov.:
30
AF XY:
0.00000148
AC XY:
1
AN XY:
674512
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
29690
American (AMR)
AF:
0.00
AC:
0
AN:
34076
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24290
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34474
South Asian (SAS)
AF:
0.0000129
AC:
1
AN:
77716
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
33914
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4304
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1072178
Other (OTH)
AF:
0.00
AC:
0
AN:
57036
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
33

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jul 08, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
7.9
DANN
Benign
0.92
PhyloP100
1.1
PromoterAI
0.016
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.9
Mutation Taster
=100/0
polymorphism

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

Other links and lift over

dbSNP: rs1654412142; hg19: chr1-207495125; API