rs6470475

chr8-126819046-C-Achr8-126819046-C-G

Variant summary

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

The ENST00000520224.2(ENSG00000253573):n.440-24719G>T 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 0.501 in 151,434 control chromosomes in the GnomAD database, including 19,754 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 (19754 hom., cov: 31)
• Consequence: ENST00000520224.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375753	XR_928636.3	n.237+26225G>T		intron_variant, non_coding_transcript_variant
LOC105375751	XR_007061098.1	n.657-46382C>A		intron_variant, non_coding_transcript_variant
LOC105375753	XR_928638.3	n.199+26225G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000520224.2	n.440-24719G>T		intron_variant, non_coding_transcript_variant		3
PCAT1	ENST00000645463.1	n.673-58626C>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645198.1	n.22-58626C>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000647190.2	n.474-58626C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75871 AN: 151320 Hom.: 19751 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.464

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.501 AC: 75902 AN: 151434 Hom.: 19754 Cov.: 31 AF XY: 0.502 AC XY: 37119 AN XY: 73990

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.501

Alfa AF: 0.511 Hom.: 6957

Bravo AF: 0.496

Asia WGS AF: 0.470 AC: 1618 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.2
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6470475; hg19: chr8-127831291;