rs17197199
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The ENST00000441888.7(POU5F1):c.-183-4648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 1,466,142 control chromosomes in the GnomAD database, including 2,348 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 0.072 ( 667 hom., cov: 32)
Exomes 𝑓: 0.037 ( 1681 hom. )
Consequence
POU5F1
ENST00000441888.7 intron
ENST00000441888.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.65
Genes affected
POU5F1 (HGNC:9221): (POU class 5 homeobox 1) This gene encodes a transcription factor containing a POU homeodomain that plays a key role in embryonic development and stem cell pluripotency. Aberrant expression of this gene in adult tissues is associated with tumorigenesis. This gene can participate in a translocation with the Ewing's sarcoma gene on chromosome 21, which also leads to tumor formation. Alternative splicing, as well as usage of alternative AUG and non-AUG translation initiation codons, results in multiple isoforms. One of the AUG start codons is polymorphic in human populations. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU5F1 | NM_002701.6 | upstream_gene_variant | ENST00000259915.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU5F1 | ENST00000441888.7 | c.-183-4648G>A | intron_variant | 1 | |||||
POU5F1 | ENST00000259915.13 | upstream_gene_variant | 1 | NM_002701.6 | P1 | ||||
POU5F1 | ENST00000461401.1 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0721 AC: 10964AN: 152084Hom.: 665 Cov.: 32
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GnomAD4 exome AF: 0.0368 AC: 48416AN: 1313938Hom.: 1681 Cov.: 32 AF XY: 0.0365 AC XY: 23332AN XY: 638742
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GnomAD4 genome ? AF: 0.0721 AC: 10975AN: 152204Hom.: 667 Cov.: 32 AF XY: 0.0728 AC XY: 5422AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at