rs980171

Variant names:

• chr8-127042277-A-G
• rs980171
• ENST00000643594.2:n.216-21771A>G

Variant summary

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

The ENST00000643594.2(PCAT1):​n.216-21771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,686 control chromosomes in the GnomAD database, including 15,607 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 0.44 (15607 hom., cov: 32)
• Consequence: PCAT1 ENST00000643594.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000643594.2	n.216-21771A>G		intron_variant	Intron 2 of 2
PCAT1	ENST00000644627.1	n.712-21771A>G		intron_variant	Intron 4 of 4
PCAT1	ENST00000644733.1	n.126-21771A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66788 AN: 151568 Hom.: 15576 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.441 AC: 66876 AN: 151686 Hom.: 15607 Cov.: 32 AF XY: 0.434 AC XY: 32217 AN XY: 74148

African (AFR) AF: 0.596 AC: 24669 AN: 41400

American (AMR) AF: 0.434 AC: 6605 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1221 AN: 3460

East Asian (EAS) AF: 0.224 AC: 1143 AN: 5108

South Asian (SAS) AF: 0.391 AC: 1883 AN: 4820

European-Finnish (FIN) AF: 0.294 AC: 3113 AN: 10590

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.396 AC: 26840 AN: 67768

Other (OTH) AF: 0.461 AC: 969 AN: 2104

Alfa AF: 0.415 Hom.: 45580

Bravo AF: 0.458

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.4
DANN	Benign	0.62
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs980171; hg19: chr8-128054522;