rs12610185
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025245.3(PBX4):c.119+7598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,198 control chromosomes in the GnomAD database, including 621 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 0.087 ( 621 hom., cov: 32)
Consequence
PBX4
NM_025245.3 intron
NM_025245.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.162
Genes affected
PBX4 (HGNC:13403): (PBX homeobox 4) This gene encodes a member of the pre-B cell leukemia transcription factor family. These proteins are homeobox proteins that play critical roles in embryonic development and cellular differentiation both as Hox cofactors and through Hox-independent pathways. The encoded protein contains a homeobox DNA-binding domain, but specific functions of the protein have not been determined. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, May 2011]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PBX4 | NM_025245.3 | c.119+7598C>T | intron_variant | ENST00000251203.14 | NP_079521.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PBX4 | ENST00000251203.14 | c.119+7598C>T | intron_variant | 1 | NM_025245.3 | ENSP00000251203 | P1 | |||
PBX4 | ENST00000557978.6 | c.119+7598C>T | intron_variant, NMD_transcript_variant | 1 | ENSP00000453348 | |||||
PBX4 | ENST00000558222.1 | c.119+7598C>T | intron_variant, NMD_transcript_variant | 2 | ENSP00000453069 |
Frequencies
GnomAD3 genomes AF: 0.0871 AC: 13252AN: 152080Hom.: 612 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0873 AC: 13285AN: 152198Hom.: 621 Cov.: 32 AF XY: 0.0882 AC XY: 6564AN XY: 74406
GnomAD4 genome
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565
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at