rs3219018
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004001.5(FCGR2B):c.-72-314G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: not found (cov: 0)
Failed GnomAD Quality Control
Consequence
FCGR2B
NM_004001.5 intron
NM_004001.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0560
Publications
28 publications found
Genes affected
FCGR2B (HGNC:3618): (Fc gamma receptor IIb) The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]
FCGR2B Gene-Disease associations (from GenCC):
- systemic lupus erythematosusInheritance: Unknown Classification: SUPPORTIVE, NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FCGR2B | NM_004001.5 | c.-72-314G>C | intron_variant | Intron 1 of 8 | NP_003992.3 | |||
| FCGR2B | NM_001002275.3 | c.-72-314G>C | intron_variant | Intron 1 of 8 | NP_001002275.1 | |||
| FCGR2B | NM_001190828.2 | c.-72-314G>C | intron_variant | Intron 1 of 7 | NP_001177757.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|
Frequencies
GnomAD3 genomes 0 Cov.: 0
GnomAD3 genomes
AC:
0
AN:
0
Hom.:
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
Alfa
AF:
Hom.:
ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Systemic lupus erythematosus, susceptibility to Other:1
Jul 01, 2005
OMIM
Significance:risk factor
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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