rs1061118
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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.1047C>T(p.Ser349=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 1,581,374 control chromosomes in the GnomAD database, including 353,998 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 0.69 ( 36738 hom., cov: 31)
Exomes 𝑓: 0.66 ( 317260 hom. )
Consequence
POU5F1
NM_002701.6 synonymous
NM_002701.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00800
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP7
?
Synonymous conserved (PhyloP=0.008 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU5F1 | NM_002701.6 | c.1047C>T | p.Ser349= | synonymous_variant | 5/5 | ENST00000259915.13 | |
POU5F1 | NM_001173531.3 | c.537C>T | p.Ser179= | synonymous_variant | 5/5 | ||
POU5F1 | NM_203289.6 | c.537C>T | p.Ser179= | synonymous_variant | 4/4 | ||
POU5F1 | NM_001285986.2 | c.459C>T | p.Ser153= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU5F1 | ENST00000259915.13 | c.1047C>T | p.Ser349= | synonymous_variant | 5/5 | 1 | NM_002701.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.691 AC: 104888AN: 151832Hom.: 36709 Cov.: 31
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GnomAD3 exomes AF: 0.636 AC: 114474AN: 180008Hom.: 36722 AF XY: 0.633 AC XY: 61221AN XY: 96642
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GnomAD4 exome AF: 0.664 AC: 949796AN: 1429426Hom.: 317260 Cov.: 52 AF XY: 0.661 AC XY: 468185AN XY: 707962
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GnomAD4 genome ? AF: 0.691 AC: 104965AN: 151948Hom.: 36738 Cov.: 31 AF XY: 0.685 AC XY: 50837AN XY: 74256
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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
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