rs1428102803

Variant names:

• chr8-127193633-G-T
• rs1428102803
• ENST00000641001.1:n.324-5518C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_120364.1(CASC19):​n.153+3842C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 151,392 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.0048 (2 hom., cov: 30)
• Consequence: CASC19 NR_120364.1 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.89
• Publications: 1 publications found

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120364.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	NR_120364.1		n.153+3842C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	ENST00000641001.1		n.324-5518C>A		intron	N/A
	CASC19	ENST00000641013.1		n.256-5518C>A		intron	N/A
	CASC19	ENST00000641029.1		n.219-3651C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00484 AC: 732 AN: 151278 Hom.: 2 Cov.: 30

Gnomad AFR AF: 0.00109

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00145

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000582

Gnomad SAS AF: 0.00229

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00730

Gnomad OTH AF: 0.00145

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

GnomAD4 genome AF: 0.00484 AC: 732 AN: 151392 Hom.: 2 Cov.: 30 AF XY: 0.00507 AC XY: 375 AN XY: 73940

African (AFR) AF: 0.00109 AC: 45 AN: 41312

American (AMR) AF: 0.00145 AC: 22 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3456

East Asian (EAS) AF: 0.000583 AC: 3 AN: 5144

South Asian (SAS) AF: 0.00229 AC: 11 AN: 4802

European-Finnish (FIN) AF: 0.0145 AC: 153 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00731 AC: 494 AN: 67618

Other (OTH) AF: 0.00143 AC: 3 AN: 2096

Alfa AF: 0.00674 Hom.: 0

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Familial prostate cancer (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1428102803; hg19: chr8-128205878;