ENST00000523510.1:n.350+1167A>G

Variant names:

• chr8-127075659-T-C
• rs6470494
• ENST00000523510.1:n.350+1167A>G

Variant summary

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

The ENST00000523510.1(CASC19):​n.350+1167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,040 control chromosomes in the GnomAD database, including 39,074 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 0.72 (39074 hom., cov: 32)
• Consequence: CASC19 ENST00000523510.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

CASC19 (HGNC:49476): (cancer susceptibility 19)

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]

PCAT2 (HGNC:45089): (prostate cancer associated transcript 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCAT2	NR_119373.1	n.350+1167A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000523510.1	n.350+1167A>G		intron_variant	Intron 3 of 3	3
PCAT1	ENST00000645463.1	n.855+69041T>C		intron_variant	Intron 6 of 6
PCAT1	ENST00000646670.1	n.1064+61885T>C		intron_variant	Intron 5 of 6
PCAT1	ENST00000647190.2	n.1191+26359T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108913 AN: 151922 Hom.: 39059 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.717 AC: 108987 AN: 152040 Hom.: 39074 Cov.: 32 AF XY: 0.719 AC XY: 53389 AN XY: 74304

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.729

Alfa AF: 0.720 Hom.: 31217

Bravo AF: 0.713

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6470494; hg19: chr8-128087904;