chr19-44757093-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005178.5(BCL3):āc.596T>Cā(p.Met199Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00073 in 1,608,974 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_005178.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL3 | NM_005178.5 | c.596T>C | p.Met199Thr | missense_variant | 4/9 | ENST00000164227.10 | |
BCL3 | XM_011527198.4 | c.596T>C | p.Met199Thr | missense_variant | 4/9 | ||
BCL3 | XM_017027110.2 | c.476T>C | p.Met159Thr | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL3 | ENST00000164227.10 | c.596T>C | p.Met199Thr | missense_variant | 4/9 | 1 | NM_005178.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00416 AC: 632AN: 152094Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00113 AC: 265AN: 234480Hom.: 0 AF XY: 0.000815 AC XY: 105AN XY: 128862
GnomAD4 exome AF: 0.000372 AC: 542AN: 1456762Hom.: 3 Cov.: 33 AF XY: 0.000308 AC XY: 223AN XY: 724464
GnomAD4 genome AF: 0.00415 AC: 632AN: 152212Hom.: 8 Cov.: 32 AF XY: 0.00382 AC XY: 284AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 03, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at