rs4871005

Positions:

• chr8-127001131-A-C
• chr8-127001131-A-G
• chr8-127001131-A-T

Variant summary

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

The ENST00000645463.1(PCAT1):​n.792-5424A>C 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 0.53 in 152,022 control chromosomes in the GnomAD database, including 22,683 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 (22683 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375751	XR_007061105.1	n.1735-5424A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.792-5424A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80528 AN: 151904 Hom.: 22665 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.530 AC: 80580 AN: 152022 Hom.: 22683 Cov.: 32 AF XY: 0.538 AC XY: 39975 AN XY: 74308

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.556

Alfa AF: 0.596 Hom.: 54978

Bravo AF: 0.519

Asia WGS AF: 0.602 AC: 2091 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871005; hg19: chr8-128013376;