rs4871750

Positions:

• chr8-126889758-G-A
• chr8-126889758-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645463.1(PCAT1):​n.791+11968G>A variant causes a intron, non coding transcript 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 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.791+11968G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.436

Alfa AF: 0.481 Hom.: 36304

Bravo AF: 0.421

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871750; hg19: chr8-127902003;