11-118898482-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001378213.1(BCL9L):c.4433G>A(p.Ser1478Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,604,488 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_001378213.1 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 |
---|---|---|---|---|---|---|---|---|
BCL9L | NM_001378213.1 | c.4433G>A | p.Ser1478Asn | missense_variant | Exon 10 of 10 | ENST00000683865.1 | NP_001365142.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL9L | ENST00000683865.1 | c.4433G>A | p.Ser1478Asn | missense_variant | Exon 10 of 10 | NM_001378213.1 | ENSP00000507778.1 | |||
BCL9L | ENST00000334801.7 | c.4433G>A | p.Ser1478Asn | missense_variant | Exon 8 of 8 | 1 | ENSP00000335320.3 | |||
BCL9L | ENST00000526143.2 | c.4322G>A | p.Ser1441Asn | missense_variant | Exon 8 of 8 | 5 | ENSP00000482938.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000814 AC: 2AN: 245702Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133884
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452254Hom.: 0 Cov.: 35 AF XY: 0.00000139 AC XY: 1AN XY: 720552
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4433G>A (p.S1478N) alteration is located in exon 8 (coding exon 8) of the BCL9L gene. This alteration results from a G to A substitution at nucleotide position 4433, causing the serine (S) at amino acid position 1478 to be replaced by an asparagine (N). 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