rs1265163
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000471529.6(POU5F1):c.-446G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,497,844 control chromosomes in the GnomAD database, including 13,978 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 ( 1697 hom., cov: 33)
Exomes 𝑓: 0.13 ( 12281 hom. )
Consequence
POU5F1
ENST00000471529.6 5_prime_UTR
ENST00000471529.6 5_prime_UTR
Scores
2
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.198
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]
TCF19 (HGNC:11629): (transcription factor 19) This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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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 (MetaRNN=0.0043299794).
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.406-263G>C | intron_variant | ENST00000259915.13 | |||
POU5F1 | NM_001285986.2 | c.-671G>C | 5_prime_UTR_variant | 1/3 | |||
POU5F1 | NM_203289.6 | c.-368G>C | 5_prime_UTR_variant | 1/4 | |||
POU5F1 | NM_001173531.3 | c.-106+224G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU5F1 | ENST00000259915.13 | c.406-263G>C | intron_variant | 1 | NM_002701.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 21727AN: 150522Hom.: 1693 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.144 AC: 19987AN: 138420Hom.: 1773 AF XY: 0.138 AC XY: 10342AN XY: 75034
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GnomAD4 exome AF: 0.129 AC: 173950AN: 1347202Hom.: 12281 Cov.: 85 AF XY: 0.127 AC XY: 84051AN XY: 663008
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GnomAD4 genome ? AF: 0.144 AC: 21746AN: 150642Hom.: 1697 Cov.: 33 AF XY: 0.147 AC XY: 10801AN XY: 73520
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509
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523
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
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T
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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