2-159325862-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_013450.4(BAZ2B):c.6000T>C(p.Asn2000=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000593 in 1,601,166 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000060 ( 0 hom. )
Consequence
BAZ2B
NM_013450.4 synonymous
NM_013450.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.206
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 2-159325862-A-G is Benign according to our data. Variant chr2-159325862-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3052514.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.206 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.6000T>C | p.Asn2000= | synonymous_variant | 35/37 | ENST00000392783.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.6000T>C | p.Asn2000= | synonymous_variant | 35/37 | 5 | NM_013450.4 | P1 | |
BAZ2B | ENST00000392782.5 | c.5892T>C | p.Asn1964= | synonymous_variant | 34/36 | 1 | |||
BAZ2B | ENST00000474437.1 | n.540T>C | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
BAZ2B | ENST00000548440.1 | n.514T>C | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152018Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
8
AN:
152018
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000803 AC: 19AN: 236758Hom.: 0 AF XY: 0.000117 AC XY: 15AN XY: 128282
GnomAD3 exomes
AF:
AC:
19
AN:
236758
Hom.:
AF XY:
AC XY:
15
AN XY:
128282
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000600 AC: 87AN: 1449148Hom.: 0 Cov.: 32 AF XY: 0.0000680 AC XY: 49AN XY: 720242
GnomAD4 exome
AF:
AC:
87
AN:
1449148
Hom.:
Cov.:
32
AF XY:
AC XY:
49
AN XY:
720242
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74256
GnomAD4 genome
?
AF:
AC:
8
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
5
AN XY:
74256
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
BAZ2B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 05, 2019 | This variant is classified as likely 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
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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