7-73442220-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032408.4(BAZ1B):c.4428C>T(p.Ser1476=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000647 in 1,406,456 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 0.000015 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000070 ( 0 hom. )
Consequence
BAZ1B
NM_032408.4 synonymous
NM_032408.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.819
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 7-73442220-G-A is Benign according to our data. Variant chr7-73442220-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 752384.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.819 with no splicing effect.
BS2
High AC in GnomAdExome4 at 89 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ1B | NM_032408.4 | c.4428C>T | p.Ser1476= | synonymous_variant | 19/20 | ENST00000339594.9 | |
BAZ1B | NM_001370402.1 | c.4428C>T | p.Ser1476= | synonymous_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ1B | ENST00000339594.9 | c.4428C>T | p.Ser1476= | synonymous_variant | 19/20 | 1 | NM_032408.4 | P1 | |
BAZ1B | ENST00000404251.1 | c.4428C>T | p.Ser1476= | synonymous_variant | 19/19 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000146 AC: 2AN: 137130Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250802Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135550
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GnomAD4 exome AF: 0.0000701 AC: 89AN: 1269326Hom.: 0 Cov.: 33 AF XY: 0.0000651 AC XY: 41AN XY: 629584
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GnomAD4 genome AF: 0.0000146 AC: 2AN: 137130Hom.: 0 Cov.: 31 AF XY: 0.0000152 AC XY: 1AN XY: 65582
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at