rs1178977
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032408.4(BAZ1B):c.4094+6T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,612,286 control chromosomes in the GnomAD database, including 29,469 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 0.21 ( 3732 hom., cov: 32)
Exomes 𝑓: 0.18 ( 25737 hom. )
Consequence
BAZ1B
NM_032408.4 splice_donor_region, intron
NM_032408.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0002968
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.20
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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ1B | NM_032408.4 | c.4094+6T>C | splice_donor_region_variant, intron_variant | ENST00000339594.9 | |||
BAZ1B | NM_001370402.1 | c.4094+6T>C | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ1B | ENST00000339594.9 | c.4094+6T>C | splice_donor_region_variant, intron_variant | 1 | NM_032408.4 | P1 | |||
BAZ1B | ENST00000404251.1 | c.4094+6T>C | splice_donor_region_variant, intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31498AN: 151908Hom.: 3710 Cov.: 32
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GnomAD3 exomes AF: 0.162 AC: 40684AN: 251154Hom.: 3717 AF XY: 0.159 AC XY: 21612AN XY: 135720
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GnomAD4 exome AF: 0.183 AC: 267401AN: 1460258Hom.: 25737 Cov.: 32 AF XY: 0.180 AC XY: 131021AN XY: 726384
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GnomAD4 genome ? AF: 0.208 AC: 31568AN: 152028Hom.: 3732 Cov.: 32 AF XY: 0.204 AC XY: 15188AN XY: 74320
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at