19-44749034-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005178.5(BCL3):āc.244C>Gā(p.Leu82Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,352,962 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L82F) has been classified as Uncertain significance.
Frequency
Consequence
NM_005178.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL3 | NM_005178.5 | c.244C>G | p.Leu82Val | missense_variant | 1/9 | ENST00000164227.10 | |
BCL3 | XM_011527198.4 | c.244C>G | p.Leu82Val | missense_variant | 1/9 | ||
BCL3 | XM_017027110.2 | c.136+906C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL3 | ENST00000164227.10 | c.244C>G | p.Leu82Val | missense_variant | 1/9 | 1 | NM_005178.5 | P1 | |
BCL3 | ENST00000403534.7 | n.424+906C>G | intron_variant, non_coding_transcript_variant | 2 | |||||
BCL3 | ENST00000487394.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151942Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000142 AC: 17AN: 1201020Hom.: 0 Cov.: 29 AF XY: 0.0000187 AC XY: 11AN XY: 587332
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151942Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.244C>G (p.L82V) alteration is located in exon 1 (coding exon 1) of the BCL3 gene. This alteration results from a C to G substitution at nucleotide position 244, causing the leucine (L) at amino acid position 82 to be replaced by a valine (V). 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