1-207321810-C-T
Variant names:
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.45C>T(p.Leu15Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000654 in 1,375,966 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: 0.0000065 ( 0 hom. )
Consequence
CD55
NM_000574.5 synonymous
NM_000574.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
Publications
0 publications found
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 enteropathyInheritance: 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 (REVEL=0.016).
BP6
Variant 1-207321810-C-T is Benign according to our data. Variant chr1-207321810-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3680669.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.39 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000654 AC: 9AN: 1375966Hom.: 0 Cov.: 31 AF XY: 0.00000737 AC XY: 5AN XY: 678790 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
1375966
Hom.:
Cov.:
31
AF XY:
AC XY:
5
AN XY:
678790
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30532
American (AMR)
AF:
AC:
0
AN:
35304
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24874
East Asian (EAS)
AF:
AC:
0
AN:
35014
South Asian (SAS)
AF:
AC:
0
AN:
78630
European-Finnish (FIN)
AF:
AC:
0
AN:
34614
Middle Eastern (MID)
AF:
AC:
0
AN:
4220
European-Non Finnish (NFE)
AF:
AC:
9
AN:
1075388
Other (OTH)
AF:
AC:
0
AN:
57390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 23, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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