12-122044006-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001024808.3(BCL7A):āc.392A>Gā(p.Lys131Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,613,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000066 ( 0 hom., cov: 31)
Exomes š: 0.000068 ( 0 hom. )
Consequence
BCL7A
NM_001024808.3 missense
NM_001024808.3 missense
Scores
1
5
11
Clinical Significance
Conservation
PhyloP100: 8.48
Genes affected
BCL7A (HGNC:1004): (BAF chromatin remodeling complex subunit BCL7A) This gene is directly involved, with Myc and IgH, in a three-way gene translocation in a Burkitt lymphoma cell line. As a result of the gene translocation, the N-terminal region of the gene product is disrupted, which is thought to be related to the pathogenesis of a subset of high-grade B cell non-Hodgkin lymphoma. The N-terminal segment involved in the translocation includes the region that shares a strong sequence similarity with those of BCL7B and BCL7C. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.1603998).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL7A | NM_001024808.3 | c.392A>G | p.Lys131Arg | missense_variant | 4/6 | ENST00000261822.5 | |
BCL7A | NM_020993.5 | c.392A>G | p.Lys131Arg | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL7A | ENST00000261822.5 | c.392A>G | p.Lys131Arg | missense_variant | 4/6 | 1 | NM_001024808.3 | P1 | |
BCL7A | ENST00000538010.5 | c.392A>G | p.Lys131Arg | missense_variant | 4/6 | 1 | |||
BCL7A | ENST00000432926.2 | n.506A>G | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152162Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000121 AC: 30AN: 248650Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134640
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GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461696Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727168
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152162Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74322
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.392A>G (p.K131R) alteration is located in exon 4 (coding exon 4) of the BCL7A gene. This alteration results from a A to G substitution at nucleotide position 392, causing the lysine (K) at amino acid position 131 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
D;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at