chr11-118898618-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001378213.1(BCL9L):c.4297T>A(p.Phe1433Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000726 in 1,612,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL9L | NM_001378213.1 | c.4297T>A | p.Phe1433Ile | missense_variant | 10/10 | ENST00000683865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL9L | ENST00000683865.1 | c.4297T>A | p.Phe1433Ile | missense_variant | 10/10 | NM_001378213.1 | P4 | ||
BCL9L | ENST00000334801.7 | c.4297T>A | p.Phe1433Ile | missense_variant | 8/8 | 1 | P4 | ||
BCL9L | ENST00000526143.2 | c.4186T>A | p.Phe1396Ile | missense_variant | 8/8 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000651 AC: 16AN: 245908Hom.: 0 AF XY: 0.0000746 AC XY: 10AN XY: 134030
GnomAD4 exome AF: 0.0000740 AC: 108AN: 1460196Hom.: 0 Cov.: 35 AF XY: 0.0000826 AC XY: 60AN XY: 726358
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.4297T>A (p.F1433I) alteration is located in exon 8 (coding exon 8) of the BCL9L gene. This alteration results from a T to A substitution at nucleotide position 4297, causing the phenylalanine (F) at amino acid position 1433 to be replaced by an isoleucine (I). 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