rs204994
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002586.5(PBX2):c.1024+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,611,374 control chromosomes in the GnomAD database, including 42,070 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 3480 hom., cov: 32)
Exomes 𝑓: 0.22 ( 38590 hom. )
Consequence
PBX2
NM_002586.5 intron
NM_002586.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0130
Genes affected
PBX2 (HGNC:8633): (PBX homeobox 2) This gene encodes a ubiquitously expressed member of the TALE/PBX homeobox family. It was identified by its similarity to a homeobox gene which is involved in t(1;19) translocation in acute pre-B-cell leukemias. This protein is a transcriptional activator which binds to the TLX1 promoter. The gene is located within the major histocompatibility complex (MHC) on chromosome 6. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBX2 | NM_002586.5 | c.1024+21G>A | intron_variant | ENST00000375050.6 | |||
PBX2 | XM_047418839.1 | c.679+21G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBX2 | ENST00000375050.6 | c.1024+21G>A | intron_variant | 1 | NM_002586.5 | P1 | |||
PBX2 | ENST00000478678.5 | n.1072G>A | non_coding_transcript_exon_variant | 6/6 | 1 | ||||
PBX2 | ENST00000495300.1 | n.274+21G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
PBX2 | ENST00000496171.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.208 AC: 31635AN: 151946Hom.: 3488 Cov.: 32
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GnomAD3 exomes AF: 0.177 AC: 43546AN: 245892Hom.: 4319 AF XY: 0.177 AC XY: 23771AN XY: 134046
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GnomAD4 exome AF: 0.222 AC: 324638AN: 1459308Hom.: 38590 Cov.: 33 AF XY: 0.219 AC XY: 158855AN XY: 725996
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GnomAD4 genome AF: 0.208 AC: 31638AN: 152066Hom.: 3480 Cov.: 32 AF XY: 0.200 AC XY: 14868AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at