rs5744655
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000241436.9(POLK):c.694+279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 152,308 control chromosomes in the GnomAD database, including 18 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 0.011 ( 18 hom., cov: 32)
Consequence
POLK
ENST00000241436.9 intron
ENST00000241436.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.51
Genes affected
POLK (HGNC:9183): (DNA polymerase kappa) This gene encodes a member of the DNA polymerase type-Y family of proteins. The encoded protein is a specialized DNA polymerase that catalyzes translesion DNA synthesis, which allows DNA replication in the presence of DNA lesions. Human cell lines lacking a functional copy of this gene exhibit impaired genome integrity and enhanced susceptibility to oxidative damage. Mutations in this gene that impair enzyme activity may be associated with prostate cancer in human patients. [provided by RefSeq, Sep 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 (BayesDel_noAF=-0.69).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0107 (1635/152308) while in subpopulation EAS AF= 0.0214 (111/5184). AF 95% confidence interval is 0.0182. There are 18 homozygotes in gnomad4. There are 872 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLK | NM_016218.6 | c.694+279A>G | intron_variant | ENST00000241436.9 | |||
POLK | NR_170560.3 | n.868+279A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLK | ENST00000241436.9 | c.694+279A>G | intron_variant | 1 | NM_016218.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0108 AC: 1637AN: 152190Hom.: 18 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0107 AC: 1635AN: 152308Hom.: 18 Cov.: 32 AF XY: 0.0117 AC XY: 872AN XY: 74486
GnomAD4 genome
?
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1635
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32
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872
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74486
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74
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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