2-159324887-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_013450.4(BAZ2B):c.6277C>T(p.Leu2093Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00023 in 1,554,912 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.00043 ( 0 hom., cov: 24)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
BAZ2B
NM_013450.4 missense
NM_013450.4 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 2.85
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 Benign. Variant got -7 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0063993037).
BP6
Variant 2-159324887-G-A is Benign according to our data. Variant chr2-159324887-G-A is described in ClinVar as [Benign]. Clinvar id is 3042651.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000426 (64/150064) while in subpopulation EAS AF= 0.0124 (63/5088). AF 95% confidence interval is 0.00993. There are 0 homozygotes in gnomad4. There are 31 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.6277C>T | p.Leu2093Phe | missense_variant | 36/37 | 5 | NM_013450.4 | ENSP00000376534.2 | ||
BAZ2B | ENST00000392782.5 | c.6169C>T | p.Leu2057Phe | missense_variant | 35/36 | 1 | ENSP00000376533.1 | |||
BAZ2B | ENST00000548440.1 | n.791C>T | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000427 AC: 64AN: 149948Hom.: 0 Cov.: 24
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GnomAD3 exomes AF: 0.000626 AC: 126AN: 201154Hom.: 0 AF XY: 0.000542 AC XY: 60AN XY: 110620
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GnomAD4 exome AF: 0.000209 AC: 293AN: 1404848Hom.: 1 Cov.: 29 AF XY: 0.000192 AC XY: 134AN XY: 697732
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GnomAD4 genome AF: 0.000426 AC: 64AN: 150064Hom.: 0 Cov.: 24 AF XY: 0.000423 AC XY: 31AN XY: 73202
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BAZ2B-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
P;P
Vest4
MVP
MPC
0.17
ClinPred
T
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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