rs844
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394477.1(FCGR2B):c.*190A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FCGR2B
NM_001394477.1 3_prime_UTR
NM_001394477.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0790
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCGR2B | NM_001394477.1 | c.*190A>C | 3_prime_UTR_variant | 8/8 | ENST00000358671.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCGR2B | ENST00000358671.10 | c.*190A>C | 3_prime_UTR_variant | 8/8 | 1 | NM_001394477.1 | P4 | ||
FCGR2B | ENST00000236937.13 | c.*190A>C | 3_prime_UTR_variant | 7/7 | 1 | A2 | |||
FCGR2B | ENST00000367961.8 | c.*190A>C | 3_prime_UTR_variant | 7/7 | 1 | A2 | |||
FCGR2B | ENST00000480308.5 | n.4370A>C | non_coding_transcript_exon_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 409004Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0AN XY: 213698
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
409004
Hom.:
Cov.:
4
AF XY:
AC XY:
0
AN XY:
213698
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at