19-44748923-G-C

Variant names:

• chr19-44748923-G-C
• NM_005178.5:c.133G>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_005178.5(BCL3):​c.133G>C​(p.Ala45Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000972 in 1,028,722 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 9.7e-7 (0 hom.)
• Consequence: BCL3 NM_005178.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00

Genes affected

BCL3 (HGNC:998): (BCL3 transcription coactivator) This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31944618).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL3	NM_005178.5	c.133G>C	p.Ala45Pro	missense_variant	Exon 1 of 9	ENST00000164227.10	NP_005169.2
BCL3	XM_011527198.4	c.133G>C	p.Ala45Pro	missense_variant	Exon 1 of 9		XP_011525500.3
BCL3	XM_017027110.2	c.136+795G>C		intron_variant	Intron 1 of 6		XP_016882599.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL3	ENST00000164227.10	c.133G>C	p.Ala45Pro	missense_variant	Exon 1 of 9	1	NM_005178.5	ENSP00000164227.5
BCL3	ENST00000487394.1	n.522G>C		non_coding_transcript_exon_variant	Exon 2 of 2	3
BCL3	ENST00000403534.7	n.424+795G>C		intron_variant	Intron 1 of 7	2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 9.72e-7 AC: 1 AN: 1028722 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 488468

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000113

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.43
FATHMM_MKL	Benign	0.65	D
LIST_S2	Benign	0.53	T
M_CAP	Pathogenic	0.47	D
MetaRNN	Benign	0.32	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.90	L
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.31	N
REVEL	Benign	0.079
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.026	D
Polyphen		0.97	D
Vest4		0.28
MutPred		0.34		Gain of glycosylation at A45 (P = 0.0044);
MVP		0.73
MPC		0.36
ClinPred		0.48	T
GERP RS		2.0
Varity_R		0.18
gMVP		0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-45252180;