rs204995
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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.1201-34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,599,042 control chromosomes in the GnomAD database, including 50,717 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 0.26 ( 5774 hom., cov: 31)
Exomes 𝑓: 0.24 ( 44943 hom. )
Consequence
PBX2
NM_002586.5 intron
NM_002586.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.413
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBX2 | NM_002586.5 | c.1201-34T>C | intron_variant | ENST00000375050.6 | |||
PBX2 | XM_047418839.1 | c.856-34T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBX2 | ENST00000375050.6 | c.1201-34T>C | intron_variant | 1 | NM_002586.5 | P1 | |||
PBX2 | ENST00000495300.1 | n.668T>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 39925AN: 151890Hom.: 5781 Cov.: 31
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GnomAD3 exomes AF: 0.211 AC: 52956AN: 250398Hom.: 6332 AF XY: 0.211 AC XY: 28568AN XY: 135516
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GnomAD4 exome AF: 0.243 AC: 351100AN: 1447032Hom.: 44943 Cov.: 27 AF XY: 0.240 AC XY: 172748AN XY: 720888
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GnomAD4 genome ? AF: 0.263 AC: 39935AN: 152010Hom.: 5774 Cov.: 31 AF XY: 0.255 AC XY: 18977AN XY: 74322
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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