chr11-118902116-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001378213.1(BCL9L):c.1627A>C(p.Ser543Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S543G) has been classified as Benign.
Frequency
Consequence
NM_001378213.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL9L | NM_001378213.1 | c.1627A>C | p.Ser543Arg | missense_variant | 8/10 | ENST00000683865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL9L | ENST00000683865.1 | c.1627A>C | p.Ser543Arg | missense_variant | 8/10 | NM_001378213.1 | P4 | ||
BCL9L | ENST00000334801.7 | c.1627A>C | p.Ser543Arg | missense_variant | 6/8 | 1 | P4 | ||
BCL9L | ENST00000526143.2 | c.1516A>C | p.Ser506Arg | missense_variant | 6/8 | 5 | A1 | ||
BCL9L | ENST00000530293.1 | n.41-1355A>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 36
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at