rs1456310

Positions:

• chr8-127040188-A-G
• chr8-127040188-A-T

Variant summary

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

The ENST00000645463.1(PCAT1):​n.855+33570A>G 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 0.515 in 151,636 control chromosomes in the GnomAD database, including 20,817 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 0.52 (20817 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

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 (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	XR_007061105.1	n.1799-23860A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000645463.1	n.855+33570A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78107 AN: 151518 Hom.: 20807 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.515 AC: 78130 AN: 151636 Hom.: 20817 Cov.: 32 AF XY: 0.518 AC XY: 38400 AN XY: 74104

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.490

Alfa AF: 0.555 Hom.: 15665

Bravo AF: 0.494

Asia WGS AF: 0.509 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.026
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456310; hg19: chr8-128052433;