chr2-159324908-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013450.4(BAZ2B):c.6256C>G(p.Leu2086Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000709 in 1,409,464 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Consequence
BAZ2B
NM_013450.4 missense
NM_013450.4 missense
Scores
4
4
9
Clinical Significance
Conservation
PhyloP100: 2.97
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 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.6256C>G | p.Leu2086Val | missense_variant | 36/37 | ENST00000392783.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.6256C>G | p.Leu2086Val | missense_variant | 36/37 | 5 | NM_013450.4 | P1 | |
BAZ2B | ENST00000392782.5 | c.6148C>G | p.Leu2050Val | missense_variant | 35/36 | 1 | |||
BAZ2B | ENST00000548440.1 | n.770C>G | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
GnomAD4 exome AF: 7.09e-7 AC: 1AN: 1409464Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 700160
GnomAD4 exome
AF:
AC:
1
AN:
1409464
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
700160
Gnomad4 AFR exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
Bravo
AF:
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 | Apr 16, 2020 | The alteration results in an amino acid change:_x000D_ _x000D_ The c.6256C>G (p.L2086V) alteration is located in exon 36 (coding exon 34) of the BAZ2B gene. This alteration results from a C to G substitution at nucleotide position 6256, causing the leucine (L) at amino acid position 2086 to be replaced by a valine (V). The alteration is not observed in population database:_x000D_ _x000D_ Based on data from the Genome Aggregation Database (gnomAD), the BAZ2B c.6256C>G alteration was not observed, with coverage at this position. The altered amino acid is conserved throughout evolution:_x000D_ _x000D_ The p.L2086 amino acid is conserved in available vertebrate species. The alteration is predicted tolerated by in silico modeling:_x000D_ _x000D_ The p.L2086V alteration is predicted to be tolerated by in silico analysis. 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
Benign
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MutPred
0.67
.;Loss of stability (P = 0.334);
MVP
MPC
0.28
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at