19-44749026-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005178.5(BCL3):c.236C>T(p.Pro79Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000441 in 1,361,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005178.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL3 | NM_005178.5 | c.236C>T | p.Pro79Leu | missense_variant | 1/9 | ENST00000164227.10 | NP_005169.2 | |
BCL3 | XM_011527198.4 | c.236C>T | p.Pro79Leu | missense_variant | 1/9 | XP_011525500.3 | ||
BCL3 | XM_017027110.2 | c.136+898C>T | intron_variant | XP_016882599.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL3 | ENST00000164227.10 | c.236C>T | p.Pro79Leu | missense_variant | 1/9 | 1 | NM_005178.5 | ENSP00000164227 | P1 | |
BCL3 | ENST00000403534.7 | n.424+898C>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
BCL3 | ENST00000487394.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151888Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000413 AC: 5AN: 1210084Hom.: 0 Cov.: 30 AF XY: 0.00000337 AC XY: 2AN XY: 592680
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151888Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74182
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.236C>T (p.P79L) alteration is located in exon 1 (coding exon 1) of the BCL3 gene. This alteration results from a C to T substitution at nucleotide position 236, causing the proline (P) at amino acid position 79 to be replaced by a leucine (L). 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