chr1-147619060-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004326.4(BCL9):c.905G>A(p.Gly302Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,612,716 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004326.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL9 | NM_004326.4 | c.905G>A | p.Gly302Asp | missense_variant | 8/10 | ENST00000234739.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL9 | ENST00000234739.8 | c.905G>A | p.Gly302Asp | missense_variant | 8/10 | 1 | NM_004326.4 | P2 | |
BCL9 | ENST00000683836.1 | c.905G>A | p.Gly302Asp | missense_variant | 8/10 | ||||
BCL9 | ENST00000684121.1 | c.683G>A | p.Gly228Asp | missense_variant | 6/8 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00171 AC: 260AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00110 AC: 275AN: 249326Hom.: 1 AF XY: 0.00123 AC XY: 166AN XY: 134758
GnomAD4 exome AF: 0.00126 AC: 1837AN: 1460524Hom.: 5 Cov.: 31 AF XY: 0.00132 AC XY: 961AN XY: 726512
GnomAD4 genome AF: 0.00171 AC: 260AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00175 AC XY: 130AN XY: 74410
ClinVar
Submissions by phenotype
BCL9-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at