chr8-126889404-G-A

Variant names:

• chr8-126889404-G-A
• rs6984837
• ENST00000519319.2:n.262+10924G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519319.2(PCAT1):​n.262+10924G>A variant causes a intron 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 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.663+11614G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.262+10924G>A		intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1	n.9+10924G>A		intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1	n.161+11614G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.913 AC: 37937 AN: 41544

American (AMR) AF: 0.683 AC: 10428 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3468

East Asian (EAS) AF: 0.812 AC: 4213 AN: 5190

South Asian (SAS) AF: 0.634 AC: 3053 AN: 4812

European-Finnish (FIN) AF: 0.674 AC: 7118 AN: 10562

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45906 AN: 67962

Other (OTH) AF: 0.749 AC: 1583 AN: 2114

Alfa AF: 0.691 Hom.: 55079

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6984837; hg19: chr8-127901649;