chr1-147611852-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004326.4(BCL9):c.16C>A(p.Pro6Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,613,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004326.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL9 | NM_004326.4 | c.16C>A | p.Pro6Thr | missense_variant | Exon 4 of 10 | ENST00000234739.8 | NP_004317.2 | |
LOC128071544 | NM_001414892.1 | c.*56C>A | downstream_gene_variant | NP_001401821.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL9 | ENST00000234739.8 | c.16C>A | p.Pro6Thr | missense_variant | Exon 4 of 10 | 1 | NM_004326.4 | ENSP00000234739.3 | ||
ENSG00000288626 | ENST00000675347.1 | c.*56C>A | downstream_gene_variant | ENSP00000502794.1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250820Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135626
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727244
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.16C>A (p.P6T) alteration is located in exon 4 (coding exon 1) of the BCL9 gene. This alteration results from a C to A substitution at nucleotide position 16, causing the proline (P) at amino acid position 6 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at