2-159332687-C-G
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePM2PP3_StrongPP5_Moderate
The NM_013450.4(BAZ2B):c.5797-1G>C variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_013450.4 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.5797-1G>C | splice_acceptor_variant | ENST00000392783.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.5797-1G>C | splice_acceptor_variant | 5 | NM_013450.4 | P1 | |||
BAZ2B | ENST00000392782.5 | c.5689-1G>C | splice_acceptor_variant | 1 | |||||
BAZ2B | ENST00000548440.1 | n.310G>C | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
BAZ2B | ENST00000474437.1 | n.337-1G>C | splice_acceptor_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
BAZ2B-related Neurodevelopmental disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Feb 06, 2023 | _x000D_This variant was identified together with the variants: NM_013450.4:c.319_320del and NM_020822.3:c.2686A>G. Criteria applied: PVS1, PM2_SUP - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.