Variant chr8-127273163-GATAA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NR_117099.1(CASC21):n.148+28384_148+28387delATAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00391 in 152,146 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.0039 ( 1 hom., cov: 32)

Consequence

CASC21
NR_117099.1 intron

Scores

Not classified

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 0.479

Variant links:

Genes affected

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]

PCAT1 links:

CASC21 (HGNC:49836): (cancer susceptibility 21)

CASC21 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC21	NR_117099.1 linkuse as main transcript	n.148+28384_148+28387delATAA		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
PCAT1	ENST00000644021.1 linkuse as main transcript	n.148+28380_148+28383delATAA	intron_variant
PCAT1	ENST00000645463.1 linkuse as main transcript	n.856-19648_856-19645delATAA	intron_variant
PCAT1	ENST00000646670.1 linkuse as main transcript	n.1065-66117_1065-66114delATAA	intron_variant
PCAT1	ENST00000647190.2 linkuse as main transcript	n.1192-19648_1192-19645delATAA	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00392

AC:

596

AN:

152028

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000894

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.000917

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00146

Gnomad FIN

AF:

0.0116

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00603

Gnomad OTH

AF:

0.00144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.00391

AC:

595

AN:

152146

Hom.:

Cov.:

AF XY:

0.00398

AC XY:

296

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.000891

Gnomad4 AMR

AF:

0.000916

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.0116

Gnomad4 NFE

AF:

0.00603

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00513

Hom.:

Bravo

AF:

0.00306

Asia WGS

AF:

0.000868

AC:

AN:

3472

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Familial prostate cancer

Other:1

association, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over