chr8-127086921-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_109833.1(PRNCR1):n.7048C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 151,942 control chromosomes in the GnomAD database, including 50,257 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 0.81 ( 50257 hom., cov: 29)
Exomes 𝑓: 0.84 ( 513628 hom. )
Failed GnomAD Quality Control
Consequence
PRNCR1
NR_109833.1 non_coding_transcript_exon
NR_109833.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.54
Genes affected
PRNCR1 (HGNC:48942): (prostate cancer associated non-coding RNA 1)
CASC19 (HGNC:49476): (cancer susceptibility 19)
PCAT1 (HGNC:43022): (prostate cancer associated transcript 1) This gene produces a long non-coding RNA that promotes cell proliferation and is upregulated in prostate, colorectal, and other cancers. This RNA negatively regulates the BRCA2 tumor suppressor protein and positively regulates Myc oncoprotein. It contains binding sites for microRNAs, and may act as a sponge for microRNAs that regulate cell growth pathways. [provided by RefSeq, Dec 2017]
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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=-0.64).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRNCR1 | NR_109833.1 | n.7048C>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000519282.1 | n.590G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
PRNCR1 | ENST00000635449.1 | n.7048C>T | non_coding_transcript_exon_variant | 1/1 | |||||
CASC19 | ENST00000642100.1 | n.418-7788G>A | intron_variant, non_coding_transcript_variant | ||||||
PCAT1 | ENST00000645463.1 | n.855+80303C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.811 AC: 123169AN: 151824Hom.: 50244 Cov.: 29
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.837 AC: 1223136AN: 1460952Hom.: 513628 Cov.: 68 AF XY: 0.838 AC XY: 608961AN XY: 726814
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.811 AC: 123225AN: 151942Hom.: 50257 Cov.: 29 AF XY: 0.809 AC XY: 60107AN XY: 74256
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at