chr2-159325791-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013450.4(BAZ2B):c.6071G>A(p.Ser2024Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,606,358 control chromosomes in the GnomAD database, including 41,452 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_013450.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAZ2B | NM_013450.4 | c.6071G>A | p.Ser2024Asn | missense_variant | 35/37 | ENST00000392783.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAZ2B | ENST00000392783.7 | c.6071G>A | p.Ser2024Asn | missense_variant | 35/37 | 5 | NM_013450.4 | P1 | |
BAZ2B | ENST00000392782.5 | c.5963G>A | p.Ser1988Asn | missense_variant | 34/36 | 1 | |||
BAZ2B | ENST00000474437.1 | n.611G>A | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
BAZ2B | ENST00000548440.1 | n.585G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.239 AC: 36256AN: 151818Hom.: 4432 Cov.: 32
GnomAD3 exomes AF: 0.222 AC: 54118AN: 243724Hom.: 6255 AF XY: 0.226 AC XY: 29856AN XY: 132206
GnomAD4 exome AF: 0.223 AC: 324086AN: 1454422Hom.: 37013 Cov.: 33 AF XY: 0.224 AC XY: 161927AN XY: 723164
GnomAD4 genome ? AF: 0.239 AC: 36297AN: 151936Hom.: 4439 Cov.: 32 AF XY: 0.240 AC XY: 17855AN XY: 74272
ClinVar
Submissions by phenotype
BAZ2B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at