8-126810440-C-T

Variant summary

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

The ENST00000520224.2(ENSG00000253573):n.440-16113G>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 0.504 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: ENST00000520224.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713

Genes affected

(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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375753	XR_928636.3	n.237+34831G>A		intron_variant, non_coding_transcript_variant
LOC105375751	XR_007061098.1	n.657-54988C>T		intron_variant, non_coding_transcript_variant
LOC105375753	XR_928638.3	n.199+34831G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000520224.2	n.440-16113G>A		intron_variant, non_coding_transcript_variant		3
PCAT1	ENST00000645463.1	n.673-67232C>T		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645198.1	n.22-67232C>T		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000647190.2	n.474-67232C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.516

Alfa AF: 0.426 Hom.: 15579

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7842598; hg19: chr8-127822685;