chr2-159434566-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013450.4(BAZ2B):c.1294-1203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,874 control chromosomes in the GnomAD database, including 9,800 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 9799 hom., cov: 32)
Exomes 𝑓: 0.50 ( 1 hom. )
Consequence
BAZ2B
NM_013450.4 intron
NM_013450.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.317
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.1294-1203G>A | intron_variant | ENST00000392783.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.1294-1203G>A | intron_variant | 5 | NM_013450.4 | P1 | |||
BAZ2B | ENST00000392782.5 | c.1288-1203G>A | intron_variant | 1 | |||||
BAZ2B | ENST00000472953.1 | n.988G>A | non_coding_transcript_exon_variant | 1/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.324 AC: 49210AN: 151748Hom.: 9795 Cov.: 32
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GnomAD4 exome AF: 0.500 AC: 4AN: 8Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1AN XY: 4
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GnomAD4 genome AF: 0.324 AC: 49232AN: 151866Hom.: 9799 Cov.: 32 AF XY: 0.314 AC XY: 23290AN XY: 74232
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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