rs17400042
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_032408.4(BAZ1B):c.892-3651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0208 in 152,324 control chromosomes in the GnomAD database, including 44 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 0.021 ( 44 hom., cov: 32)
Consequence
BAZ1B
NM_032408.4 intron
NM_032408.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.13
Genes affected
BAZ1B (HGNC:961): (bromodomain adjacent to zinc finger domain 1B) This gene encodes a member of the bromodomain protein family. The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. This gene is deleted in Williams-Beuren syndrome, a developmental disorder caused by deletion of multiple genes at 7q11.23. [provided by RefSeq, Jul 2008]
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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=-0.82).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0208 (3168/152324) while in subpopulation NFE AF= 0.0307 (2091/68020). AF 95% confidence interval is 0.0296. There are 44 homozygotes in gnomad4. There are 1574 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3168 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ1B | NM_032408.4 | c.892-3651T>C | intron_variant | ENST00000339594.9 | |||
BAZ1B | NM_001370402.1 | c.892-3651T>C | intron_variant | ||||
BAZ1B | XM_047421016.1 | c.892-3651T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ1B | ENST00000339594.9 | c.892-3651T>C | intron_variant | 1 | NM_032408.4 | P1 | |||
BAZ1B | ENST00000404251.1 | c.892-3651T>C | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0208 AC: 3168AN: 152206Hom.: 45 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0208 AC: 3168AN: 152324Hom.: 44 Cov.: 32 AF XY: 0.0211 AC XY: 1574AN XY: 74486
GnomAD4 genome
?
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3168
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152324
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32
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1574
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74486
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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