chr8-127175774-G-A

Variant names:

• chr8-127175774-G-A
• rs2466024
• ENST00000641001.1:n.1439-1410C>T

Variant summary

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

The ENST00000641001.1(CASC19):​n.1439-1410C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,108 control chromosomes in the GnomAD database, including 16,968 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 0.46 (16968 hom., cov: 33)
• Consequence: CASC19 ENST00000641001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 21 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641001.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	ENST00000641001.1		n.1439-1410C>T		intron	N/A
	CASC19	ENST00000641013.1		n.427-1410C>T		intron	N/A
	CASC19	ENST00000641029.1		n.463-1410C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69932 AN: 151988 Hom.: 16933 Cov.: 33

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.460 AC: 70025 AN: 152108 Hom.: 16968 Cov.: 33 AF XY: 0.457 AC XY: 33967 AN XY: 74358

African (AFR) AF: 0.618 AC: 25634 AN: 41508

American (AMR) AF: 0.442 AC: 6761 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3464

East Asian (EAS) AF: 0.518 AC: 2681 AN: 5174

South Asian (SAS) AF: 0.332 AC: 1598 AN: 4812

European-Finnish (FIN) AF: 0.346 AC: 3662 AN: 10570

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27004 AN: 67970

Other (OTH) AF: 0.450 AC: 951 AN: 2114

Alfa AF: 0.421 Hom.: 20089

Bravo AF: 0.476

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2466024; hg19: chr8-128188019;