rs1378897

Positions:

• chr8-127110414-C-T

Variant summary

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

The ENST00000642100.1(CASC19):​n.418-31281G>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 0.0606 in 152,188 control chromosomes in the GnomAD database, including 445 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 0.061 (445 hom., cov: 32)
• Consequence: CASC19 ENST00000642100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC19	ENST00000642100.1	n.418-31281G>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+103796C>T		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000646670.1	n.1064+96640C>T		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000647190.2	n.1191+61114C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9219 AN: 152070 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0701

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

GnomAD4 genome AF: 0.0606 AC: 9215 AN: 152188 Hom.: 445 Cov.: 32 AF XY: 0.0635 AC XY: 4723 AN XY: 74408

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0927

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.0644

Gnomad4 OTH AF: 0.0708

Alfa AF: 0.0664 Hom.: 228

Bravo AF: 0.0574

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378897; hg19: chr8-128122659;