chr19-1090804-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002695.5(POLR2E):c.429+104T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 972,496 control chromosomes in the GnomAD database, including 275,264 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 0.77 ( 45630 hom., cov: 32)
Exomes 𝑓: 0.74 ( 229634 hom. )
Consequence
POLR2E
NM_002695.5 intron
NM_002695.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.24
Genes affected
POLR2E (HGNC:9192): (RNA polymerase II, I and III subunit E) This gene encodes the fifth largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. This subunit is shared by the other two DNA-directed RNA polymerases and is present in two-fold molar excess over the other polymerase subunits. An interaction between this subunit and a hepatitis virus transactivating protein has been demonstrated, suggesting that interaction between transcriptional activators and the polymerase can occur through this subunit. A pseudogene is located on chromosome 11. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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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=-1.0).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLR2E | NM_002695.5 | c.429+104T>C | intron_variant | ENST00000615234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLR2E | ENST00000615234.5 | c.429+104T>C | intron_variant | 1 | NM_002695.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.770 AC: 117092AN: 151974Hom.: 45591 Cov.: 32
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GnomAD4 exome AF: 0.744 AC: 610676AN: 820404Hom.: 229634 AF XY: 0.744 AC XY: 312426AN XY: 419908
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GnomAD4 genome ? AF: 0.770 AC: 117179AN: 152092Hom.: 45630 Cov.: 32 AF XY: 0.767 AC XY: 57002AN XY: 74348
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at