1-147618841-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_004326.4(BCL9):āc.686A>Gā(p.Asn229Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,568,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004326.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL9 | NM_004326.4 | c.686A>G | p.Asn229Ser | missense_variant | 8/10 | ENST00000234739.8 | NP_004317.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL9 | ENST00000234739.8 | c.686A>G | p.Asn229Ser | missense_variant | 8/10 | 1 | NM_004326.4 | ENSP00000234739 | P2 | |
BCL9 | ENST00000683836.1 | c.686A>G | p.Asn229Ser | missense_variant | 8/10 | ENSP00000506908 | ||||
BCL9 | ENST00000684121.1 | c.464A>G | p.Asn155Ser | missense_variant | 6/8 | ENSP00000507238 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000377 AC: 8AN: 211976Hom.: 0 AF XY: 0.0000352 AC XY: 4AN XY: 113626
GnomAD4 exome AF: 0.0000198 AC: 28AN: 1416286Hom.: 0 Cov.: 31 AF XY: 0.0000171 AC XY: 12AN XY: 701112
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.686A>G (p.N229S) alteration is located in exon 8 (coding exon 5) of the BCL9 gene. This alteration results from a A to G substitution at nucleotide position 686, causing the asparagine (N) at amino acid position 229 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | BCL9: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at