rs6993569

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000645463.1(PCAT1):​n.855+65234G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,046 control chromosomes in the GnomAD database, including 4,839 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 0.19 ( 4839 hom., cov: 32)

Consequence

PCAT1
ENST00000645463.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583
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]

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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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCAT1ENST00000645463.1 linkuse as main transcriptn.855+65234G>A intron_variant, non_coding_transcript_variant
PCAT1ENST00000646670.1 linkuse as main transcriptn.1064+58078G>A intron_variant, non_coding_transcript_variant
PCAT1ENST00000647190.2 linkuse as main transcriptn.1191+22552G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.187
AC:
28382
AN:
151930
Hom.:
4823
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.0504
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.0481
Gnomad EAS
AF:
0.285
Gnomad SAS
AF:
0.124
Gnomad FIN
AF:
0.0757
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.0587
Gnomad OTH
AF:
0.162
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.187
AC:
28449
AN:
152046
Hom.:
4839
Cov.:
32
AF XY:
0.188
AC XY:
13994
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.0481
Gnomad4 EAS
AF:
0.284
Gnomad4 SAS
AF:
0.124
Gnomad4 FIN
AF:
0.0757
Gnomad4 NFE
AF:
0.0587
Gnomad4 OTH
AF:
0.166
Alfa
AF:
0.0806
Hom.:
1877
Bravo
AF:
0.205
Asia WGS
AF:
0.232
AC:
805
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.51
DANN
Benign
0.38

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.

Other links and lift over

dbSNP: rs6993569; hg19: chr8-128084097; API