2-159325814-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013450.4(BAZ2B):c.6048T>A(p.Asp2016Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,609,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013450.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.6048T>A | p.Asp2016Glu | missense_variant | 35/37 | ENST00000392783.7 | NP_038478.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.6048T>A | p.Asp2016Glu | missense_variant | 35/37 | 5 | NM_013450.4 | ENSP00000376534.2 | ||
BAZ2B | ENST00000392782.5 | c.5940T>A | p.Asp1980Glu | missense_variant | 34/36 | 1 | ENSP00000376533.1 | |||
BAZ2B | ENST00000474437.1 | n.588T>A | non_coding_transcript_exon_variant | 4/4 | 3 | |||||
BAZ2B | ENST00000548440.1 | n.562T>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 245270Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 133012
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1457830Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 724952
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.6048T>A (p.D2016E) alteration is located in exon 35 (coding exon 33) of the BAZ2B gene. This alteration results from a T to A substitution at nucleotide position 6048, causing the aspartic acid (D) at amino acid position 2016 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at