6-31170594-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002701.6(POU5F1):c.27C>T(p.Phe9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,560,906 control chromosomes in the GnomAD database, including 14,651 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 0.14 ( 1715 hom., cov: 33)
Exomes 𝑓: 0.13 ( 12936 hom. )
Consequence
POU5F1
NM_002701.6 synonymous
NM_002701.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.49
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP7
Synonymous conserved (PhyloP=-2.49 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU5F1 | NM_002701.6 | c.27C>T | p.Phe9= | synonymous_variant | 1/5 | ENST00000259915.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU5F1 | ENST00000259915.13 | c.27C>T | p.Phe9= | synonymous_variant | 1/5 | 1 | NM_002701.6 | P1 | |
POU5F1 | ENST00000441888.7 | c.-183-4547C>T | intron_variant | 1 | |||||
POU5F1 | ENST00000461401.1 | n.65C>T | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21820AN: 152032Hom.: 1711 Cov.: 33
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GnomAD3 exomes AF: 0.138 AC: 22752AN: 164462Hom.: 1913 AF XY: 0.132 AC XY: 11790AN XY: 89154
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GnomAD4 exome AF: 0.129 AC: 181581AN: 1408756Hom.: 12936 Cov.: 84 AF XY: 0.126 AC XY: 88020AN XY: 696150
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GnomAD4 genome AF: 0.144 AC: 21838AN: 152150Hom.: 1715 Cov.: 33 AF XY: 0.146 AC XY: 10854AN XY: 74388
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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