chr1-147618808-G-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004326.4(BCL9):c.661-8G>T 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 0.0038 in 1,513,868 control chromosomes in the GnomAD database, including 20 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 (★★).
Frequency
Consequence
NM_004326.4 splice_region, splice_polypyrimidine_tract, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL9 | NM_004326.4 | c.661-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000234739.8 | NP_004317.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL9 | ENST00000234739.8 | c.661-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004326.4 | ENSP00000234739 | P2 | |||
BCL9 | ENST00000683836.1 | c.661-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000506908 | ||||||
BCL9 | ENST00000684121.1 | c.439-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000507238 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00211 AC: 321AN: 151944Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00170 AC: 302AN: 177400Hom.: 0 AF XY: 0.00183 AC XY: 172AN XY: 93792
GnomAD4 exome AF: 0.00399 AC: 5430AN: 1361806Hom.: 20 Cov.: 30 AF XY: 0.00389 AC XY: 2600AN XY: 667924
GnomAD4 genome AF: 0.00211 AC: 321AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.00183 AC XY: 136AN XY: 74324
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | BCL9: BP4, BS1 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at