chr19-44748924-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005178.5(BCL3):c.134C>T(p.Ala45Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000593 in 1,180,920 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A45D) has been classified 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL3 | NM_005178.5 | c.134C>T | p.Ala45Val | missense_variant | 1/9 | ENST00000164227.10 | |
BCL3 | XM_011527198.4 | c.134C>T | p.Ala45Val | missense_variant | 1/9 | ||
BCL3 | XM_017027110.2 | c.136+796C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL3 | ENST00000164227.10 | c.134C>T | p.Ala45Val | missense_variant | 1/9 | 1 | NM_005178.5 | P1 | |
BCL3 | ENST00000487394.1 | n.523C>T | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
BCL3 | ENST00000403534.7 | n.424+796C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000200 AC: 3AN: 149824Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000388 AC: 4AN: 1031096Hom.: 0 Cov.: 30 AF XY: 0.00000204 AC XY: 1AN XY: 489708
GnomAD4 genome AF: 0.0000200 AC: 3AN: 149824Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1AN XY: 73074
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.134C>T (p.A45V) 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 134, causing the alanine (A) at amino acid position 45 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