chr8-126889758-G-A

Variant names:

• chr8-126889758-G-A
• rs4871750
• ENST00000519319.2:n.262+11278G>A

Variant summary

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

The ENST00000519319.2(PCAT1):​n.262+11278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,780 control chromosomes in the GnomAD database, including 14,880 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 0.44 (14880 hom., cov: 31)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519319.2. 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.663+11968G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT1	ENST00000519319.2	TSL:2	n.262+11278G>A		intron	N/A
	PCAT1	ENST00000643079.1		n.9+11278G>A		intron	N/A
	PCAT1	ENST00000643101.1		n.161+11968G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65994 AN: 151662 Hom.: 14864 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.435 AC: 66062 AN: 151780 Hom.: 14880 Cov.: 31 AF XY: 0.437 AC XY: 32410 AN XY: 74158

African (AFR) AF: 0.312 AC: 12933 AN: 41404

American (AMR) AF: 0.391 AC: 5948 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1727 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2475 AN: 5160

South Asian (SAS) AF: 0.443 AC: 2128 AN: 4804

European-Finnish (FIN) AF: 0.539 AC: 5671 AN: 10530

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33571 AN: 67886

Other (OTH) AF: 0.436 AC: 917 AN: 2102

Alfa AF: 0.470 Hom.: 57396

Bravo AF: 0.421

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.75
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4871750; hg19: chr8-127902003;