Genetic Variant ENSG00000253573:n.440-12982G>A (chr8-126807309-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000520224.2(ENSG00000253573):n.440-12982G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,822 control chromosomes in the GnomAD database, including 23,755 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 0.54 ( 23755 hom., cov: 32)

Consequence

ENSG00000253573
ENST00000520224.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.551

Variant links:

Genes affected

ENSG00000253573 (HGNC:):

ENSG00000253573 links:

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:

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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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375751	NR_188069.1 link	n.545-70363C>T	intron_variant	Intron 3 of 5
LOC105375753	XR_928636.3 link	n.238-37854G>A	intron_variant	Intron 2 of 4
LOC105375753	XR_928638.3 link	n.200-37854G>A	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000253573	ENST00000520224.2 link	n.440-12982G>A	intron_variant	Intron 2 of 7	3
PCAT1	ENST00000645198.1 link	n.22-70363C>T	intron_variant	Intron 1 of 3
PCAT1	ENST00000645463.1 link	n.673-70363C>T	intron_variant	Intron 4 of 6
PCAT1	ENST00000647190.2 link	n.474-70363C>T	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

81903

AN:

151704

Hom.:

23702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.766

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.556

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.407

Gnomad OTH

AF:

0.544

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

GnomAD4 genome

AF:

0.540

AC:

82012

AN:

151822

Hom.:

23755

Cov.:

AF XY:

0.546

AC XY:

40490

AN XY:

74144

show subpopulations

Gnomad4 AFR

AF:

0.766

Gnomad4 AMR

AF:

0.562

Gnomad4 ASJ

AF:

0.454

Gnomad4 EAS

AF:

0.600

Gnomad4 SAS

AF:

0.556

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.407

Gnomad4 OTH

AF:

0.549

Alfa

AF:

0.292

Hom.:

610

Bravo

AF:

0.558

Asia WGS

AF:

0.601

AC:

2088

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.63

DANN

Benign

0.12

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over