chr7-73444070-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_032408.4(BAZ1B):c.3904G>T(p.Gly1302Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,534 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1302R) has been classified as Uncertain significance.
Frequency
Consequence
NM_032408.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ1B | NM_032408.4 | c.3904G>T | p.Gly1302Cys | missense_variant | 17/20 | ENST00000339594.9 | |
BAZ1B | NM_001370402.1 | c.3904G>T | p.Gly1302Cys | missense_variant | 17/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ1B | ENST00000339594.9 | c.3904G>T | p.Gly1302Cys | missense_variant | 17/20 | 1 | NM_032408.4 | P1 | |
BAZ1B | ENST00000404251.1 | c.3904G>T | p.Gly1302Cys | missense_variant | 17/19 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250664Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135522
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461324Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726956
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.3904G>T (p.G1302C) alteration is located in exon 17 (coding exon 17) of the BAZ1B gene. This alteration results from a G to T substitution at nucleotide position 3904, causing the glycine (G) at amino acid position 1302 to be replaced by a cysteine (C). 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