rs3219018
Variant summary
Our verdict is Likely benign. Variant got -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
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCGR2B | NM_001002273.3 | c.-72-314G>C | intron_variant | ||||
FCGR2B | NM_001002274.3 | c.-72-314G>C | intron_variant | ||||
FCGR2B | NM_001002275.3 | c.-72-314G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 genomes
?
AF:
AC:
0
AN:
0
Hom.:
Cov.:
0
FAILED QC
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSRAC: 0AN: 0Hom.: 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
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
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2005 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at