chr2-159325687-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013450.4(BAZ2B):āc.6175A>Gā(p.Lys2059Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000314 in 1,594,326 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 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
BAZ2B
NM_013450.4 missense
NM_013450.4 missense
Scores
2
5
12
Clinical Significance
Conservation
PhyloP100: 4.31
Genes affected
BAZ2B (HGNC:963): (bromodomain adjacent to zinc finger domain 2B) This gene belongs to the bromodomain gene family. Members of this gene family encode proteins that are integral components of chromatin remodeling complexes. The encoded protein showed strong preference for the activating H3K14Ac mark in a histone peptide screen, suggesting a potential role in transcriptional activation. This gene may be associated with susceptibility to sudden cardiac death (SCD). [provided by RefSeq, Aug 2016]
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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=0.18291053).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.6175A>G | p.Lys2059Glu | missense_variant | 35/37 | ENST00000392783.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.6175A>G | p.Lys2059Glu | missense_variant | 35/37 | 5 | NM_013450.4 | P1 | |
BAZ2B | ENST00000392782.5 | c.6067A>G | p.Lys2023Glu | missense_variant | 34/36 | 1 | |||
BAZ2B | ENST00000548440.1 | n.689A>G | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000433 AC: 1AN: 231188Hom.: 0 AF XY: 0.00000796 AC XY: 1AN XY: 125648
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GnomAD4 exome AF: 0.00000139 AC: 2AN: 1442162Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 716970
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2022 | The c.6175A>G (p.K2059E) alteration is located in exon 35 (coding exon 33) of the BAZ2B gene. This alteration results from a A to G substitution at nucleotide position 6175, causing the lysine (K) at amino acid position 2059 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Pathogenic
D;D
Polyphen
P;D
Vest4
MutPred
0.33
.;Loss of ubiquitination at K2059 (P = 0.0081);
MVP
MPC
0.18
ClinPred
D
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