chr1-207552816-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_000651.6(CR1):c.3066G>A(p.Gln1022Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.000012 ( 0 hom., cov: 11)
Exomes 𝑓: 0.0000011 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CR1
NM_000651.6 synonymous
NM_000651.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.459
Publications
13 publications found
Genes affected
CR1 (HGNC:2334): (complement C3b/C4b receptor 1 (Knops blood group)) This gene is a member of the receptors of complement activation (RCA) family and is located in the 'cluster RCA' region of chromosome 1. The genome is polymorphic at this locus with allele-specific splice variants encoding different isoforms, based on the presence/absence of long homologous repeats (LHRs). The gene encodes a monomeric single-pass type I membrane glycoprotein found on erythrocytes, leukocytes, glomerular podocytes, and splenic follicular dendritic cells. The Knops blood group system is a system of antigens located on this protein. The protein mediates cellular binding to particles and immune complexes that have activated complement. Decreases in expression of this protein and/or mutations in this gene have been associated with gallbladder carcinomas, mesangiocapillary glomerulonephritis, systemic lupus erythematosus, sarcoidosis and Alzheimer's disease. Mutations in this gene have also been associated with a reduction in Plasmodium falciparum rosetting, conferring protection against severe malaria. [provided by RefSeq, May 2020]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP7
Synonymous conserved (PhyloP=-0.459 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000115 AC: 1AN: 86614Hom.: 0 Cov.: 11 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
86614
Hom.:
Cov.:
11
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000107 AC: 1AN: 935400Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0AN XY: 477500 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
935400
Hom.:
Cov.:
12
AF XY:
AC XY:
0
AN XY:
477500
show subpopulations
African (AFR)
AF:
AC:
0
AN:
25462
American (AMR)
AF:
AC:
0
AN:
36070
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21224
East Asian (EAS)
AF:
AC:
0
AN:
24960
South Asian (SAS)
AF:
AC:
0
AN:
73508
European-Finnish (FIN)
AF:
AC:
0
AN:
46956
Middle Eastern (MID)
AF:
AC:
0
AN:
3366
European-Non Finnish (NFE)
AF:
AC:
0
AN:
661932
Other (OTH)
AF:
AC:
1
AN:
41922
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000115 AC: 1AN: 86614Hom.: 0 Cov.: 11 AF XY: 0.0000241 AC XY: 1AN XY: 41462 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
86614
Hom.:
Cov.:
11
AF XY:
AC XY:
1
AN XY:
41462
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
24530
American (AMR)
AF:
AC:
0
AN:
8518
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2288
East Asian (EAS)
AF:
AC:
0
AN:
1416
South Asian (SAS)
AF:
AC:
0
AN:
1868
European-Finnish (FIN)
AF:
AC:
0
AN:
5346
Middle Eastern (MID)
AF:
AC:
0
AN:
164
European-Non Finnish (NFE)
AF:
AC:
0
AN:
40886
Other (OTH)
AF:
AC:
0
AN:
962
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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