rs147378770
Positions:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001006658.3(CR2):āc.1458T>Cā(p.Phe486=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,613,662 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0011 ( 3 hom., cov: 32)
Exomes š: 0.0013 ( 1 hom. )
Consequence
CR2
NM_001006658.3 synonymous
NM_001006658.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.766
Genes affected
CR2 (HGNC:2336): (complement C3d receptor 2) This gene encodes a membrane protein, which functions as a receptor for Epstein-Barr virus (EBV) binding on B and T lymphocytes. Genetic variations in this gene are associated with susceptibility to systemic lupus erythematosus type 9 (SLEB9). Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 1-207471052-T-C is Benign according to our data. Variant chr1-207471052-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 473094.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-207471052-T-C is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.766 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00132 (1932/1461430) while in subpopulation NFE AF= 0.00165 (1832/1111792). AF 95% confidence interval is 0.00158. There are 1 homozygotes in gnomad4_exome. There are 973 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CR2 | NM_001006658.3 | c.1458T>C | p.Phe486= | synonymous_variant | 8/20 | ENST00000367057.8 | |
CR2 | NM_001877.5 | c.1458T>C | p.Phe486= | synonymous_variant | 8/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CR2 | ENST00000367057.8 | c.1458T>C | p.Phe486= | synonymous_variant | 8/20 | 1 | NM_001006658.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152232Hom.: 3 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
163
AN:
152232
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.000828 AC: 206AN: 248768Hom.: 0 AF XY: 0.000884 AC XY: 119AN XY: 134640
GnomAD3 exomes
AF:
AC:
206
AN:
248768
Hom.:
AF XY:
AC XY:
119
AN XY:
134640
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00132 AC: 1932AN: 1461430Hom.: 1 Cov.: 33 AF XY: 0.00134 AC XY: 973AN XY: 727016
GnomAD4 exome
AF:
AC:
1932
AN:
1461430
Hom.:
Cov.:
33
AF XY:
AC XY:
973
AN XY:
727016
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00107 AC: 163AN: 152232Hom.: 3 Cov.: 32 AF XY: 0.000914 AC XY: 68AN XY: 74376
GnomAD4 genome
?
AF:
AC:
163
AN:
152232
Hom.:
Cov.:
32
AF XY:
AC XY:
68
AN XY:
74376
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CR2: BP4, BP7 - |
Immunodeficiency, common variable, 7 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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