ENST00000520224.2:n.440-24719G>T

Variant names:

• chr8-126819046-C-A
• rs6470475
• ENST00000520224.2:n.440-24719G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520224.2(ENSG00000253573):​n.440-24719G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,434 control chromosomes in the GnomAD database, including 19,754 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 0.50 (19754 hom., cov: 31)
• Consequence: ENSG00000253573 ENST00000520224.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

Genes affected

ENSG00000253573 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520224.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375751	NR_188069.1		n.545-58626C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253573	ENST00000520224.2	TSL:3	n.440-24719G>T		intron	N/A
	PCAT1	ENST00000645198.1		n.22-58626C>A		intron	N/A
	PCAT1	ENST00000645463.1		n.673-58626C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75871 AN: 151320 Hom.: 19751 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.464

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.501 AC: 75902 AN: 151434 Hom.: 19754 Cov.: 31 AF XY: 0.502 AC XY: 37119 AN XY: 73990

African (AFR) AF: 0.356 AC: 14687 AN: 41310

American (AMR) AF: 0.555 AC: 8455 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3464

East Asian (EAS) AF: 0.600 AC: 3099 AN: 5164

South Asian (SAS) AF: 0.400 AC: 1917 AN: 4798

European-Finnish (FIN) AF: 0.596 AC: 6173 AN: 10362

Middle Eastern (MID) AF: 0.472 AC: 133 AN: 282

European-Non Finnish (NFE) AF: 0.565 AC: 38295 AN: 67812

Other (OTH) AF: 0.501 AC: 1053 AN: 2100

Alfa AF: 0.516 Hom.: 8217

Bravo AF: 0.496

Asia WGS AF: 0.470 AC: 1618 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6470475; hg19: chr8-127831291;