rs6983561

Variant names:

• chr8-127094635-A-C
• rs6983561
• ENST00000642100.1:n.418-15502T>G

Variant summary

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

The ENST00000642100.1(CASC19):​n.418-15502T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,164 control chromosomes in the GnomAD database, including 4,774 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 0.16 (4774 hom., cov: 32)
• Consequence: CASC19 ENST00000642100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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
CASC19	ENST00000642100.1	n.418-15502T>G		intron_variant	Intron 1 of 1
PCAT1	ENST00000645463.1	n.855+88017A>C		intron_variant	Intron 6 of 6
PCAT1	ENST00000646670.1	n.1064+80861A>C		intron_variant	Intron 5 of 6
PCAT1	ENST00000647190.2	n.1191+45335A>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24873 AN: 152046 Hom.: 4758 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.164 AC: 24938 AN: 152164 Hom.: 4774 Cov.: 32 AF XY: 0.161 AC XY: 11976 AN XY: 74410

Gnomad4 AFR AF: 0.458 AC: 0.457702 AN: 0.457702

Gnomad4 AMR AF: 0.0702 AC: 0.0702144 AN: 0.0702144

Gnomad4 ASJ AF: 0.0389 AC: 0.0388825 AN: 0.0388825

Gnomad4 EAS AF: 0.244 AC: 0.244011 AN: 0.244011

Gnomad4 SAS AF: 0.102 AC: 0.101702 AN: 0.101702

Gnomad4 FIN AF: 0.0509 AC: 0.050932 AN: 0.050932

Gnomad4 NFE AF: 0.0324 AC: 0.0323747 AN: 0.0323747

Gnomad4 OTH AF: 0.117 AC: 0.117313 AN: 0.117313

Alfa AF: 0.0749 Hom.: 5877

Bravo AF: 0.178

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6983561; hg19: chr8-128106880;