chr8-126977604-A-C

Variant names:

• chr8-126977604-A-C
• rs901592
• ENST00000519319.2:n.263-28951A>C

Variant summary

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

The ENST00000519319.2(PCAT1):​n.263-28951A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,126 control chromosomes in the GnomAD database, including 22,627 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 0.53 (22627 hom., cov: 33)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 8 publications found

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]

LOC105375751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.664-28951A>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.263-28951A>C		intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1	n.10-28951A>C		intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1	n.162-28951A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80761 AN: 152008 Hom.: 22608 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.531 AC: 80818 AN: 152126 Hom.: 22627 Cov.: 33 AF XY: 0.538 AC XY: 40025 AN XY: 74370

African (AFR) AF: 0.338 AC: 14009 AN: 41492

American (AMR) AF: 0.600 AC: 9164 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3199 AN: 5180

South Asian (SAS) AF: 0.560 AC: 2701 AN: 4824

European-Finnish (FIN) AF: 0.647 AC: 6846 AN: 10574

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41082 AN: 67986

Other (OTH) AF: 0.559 AC: 1182 AN: 2116

Alfa AF: 0.579 Hom.: 31186

Bravo AF: 0.521

Asia WGS AF: 0.600 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.61
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs901592; hg19: chr8-127989849;