8-126810440-C-T

Variant names:

• chr8-126810440-C-T
• rs7842598
• ENST00000520224.2:n.440-16113G>A

Variant summary

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

The ENST00000520224.2(ENSG00000253573):​n.440-16113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,960 control chromosomes in the GnomAD database, including 20,623 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 (20623 hom., cov: 32)
• Consequence: ENSG00000253573 ENST00000520224.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.545-67232C>T		intron_variant	Intron 3 of 5
LOC105375753	XR_928636.3	n.237+34831G>A		intron_variant	Intron 2 of 4
LOC105375753	XR_928638.3	n.199+34831G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253573	ENST00000520224.2	n.440-16113G>A		intron_variant	Intron 2 of 7	3
PCAT1	ENST00000645198.1	n.22-67232C>T		intron_variant	Intron 1 of 3
PCAT1	ENST00000645463.1	n.673-67232C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76470 AN: 151842 Hom.: 20574 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.504 AC: 76576 AN: 151960 Hom.: 20623 Cov.: 32 AF XY: 0.507 AC XY: 37691 AN XY: 74268

African (AFR) AF: 0.697 AC: 28895 AN: 41470

American (AMR) AF: 0.536 AC: 8188 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3204 AN: 5154

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4812

European-Finnish (FIN) AF: 0.384 AC: 4051 AN: 10550

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26375 AN: 67918

Other (OTH) AF: 0.516 AC: 1089 AN: 2112

Alfa AF: 0.432 Hom.: 23403

Bravo AF: 0.526

Asia WGS AF: 0.616 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.58
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs7842598; hg19: chr8-127822685;