chr1-161630041-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001244753.2(FCGR3B):c.62-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00024 in 1,440,384 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001244753.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCGR3B | NM_001244753.2 | c.62-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000650385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCGR3B | ENST00000650385.1 | c.62-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001244753.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000285 AC: 34AN: 119368Hom.: 4 Cov.: 17
GnomAD3 exomes AF: 0.000485 AC: 102AN: 210380Hom.: 16 AF XY: 0.000453 AC XY: 52AN XY: 114756
GnomAD4 exome AF: 0.000235 AC: 311AN: 1321016Hom.: 39 Cov.: 32 AF XY: 0.000207 AC XY: 136AN XY: 656744
GnomAD4 genome ? AF: 0.000285 AC: 34AN: 119368Hom.: 4 Cov.: 17 AF XY: 0.000313 AC XY: 18AN XY: 57482
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at