rs6984837

Positions:

• chr8-126889404-G-A
• chr8-126889404-G-T

Variant summary

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

The ENST00000645463.1(PCAT1):​n.791+11614G>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 0.746 in 152,132 control chromosomes in the GnomAD database, including 43,258 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 0.75 (43258 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000645463.1	n.791+11614G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113438 AN: 152016 Hom.: 43203 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.746 AC: 113543 AN: 152132 Hom.: 43258 Cov.: 32 AF XY: 0.745 AC XY: 55429 AN XY: 74354

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.749

Alfa AF: 0.682 Hom.: 36364

Bravo AF: 0.759

Asia WGS AF: 0.688 AC: 2388 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6984837; hg19: chr8-127901649;