19-44751346-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_005178.5(BCL3):c.376G>A(p.Ala126Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000437 in 1,600,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL3 | NM_005178.5 | c.376G>A | p.Ala126Thr | missense_variant | 2/9 | ENST00000164227.10 | |
BCL3 | XM_011527198.4 | c.376G>A | p.Ala126Thr | missense_variant | 2/9 | ||
BCL3 | XM_017027110.2 | c.256G>A | p.Ala86Thr | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL3 | ENST00000164227.10 | c.376G>A | p.Ala126Thr | missense_variant | 2/9 | 1 | NM_005178.5 | P1 | |
BCL3 | ENST00000444487.1 | c.28G>A | p.Ala10Thr | missense_variant | 1/8 | 5 | |||
BCL3 | ENST00000403534.7 | n.544G>A | non_coding_transcript_exon_variant | 2/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151960Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000127 AC: 3AN: 236814Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128762
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448994Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 721038
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151960Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74210
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.376G>A (p.A126T) alteration is located in exon 2 (coding exon 2) of the BCL3 gene. This alteration results from a G to A substitution at nucleotide position 376, causing the alanine (A) at amino acid position 126 to be replaced by a threonine (T). 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