rs16901979

Variant names:

• chr8-127112671-C-A
• rs16901979
• ENST00000642100.1:n.418-33538G>T

Variant summary

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

The ENST00000642100.1(CASC19):​n.418-33538G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,144 control chromosomes in the GnomAD database, including 4,294 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 (4294 hom., cov: 32)
• Consequence: CASC19 ENST00000642100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 208 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642100.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	ENST00000642100.1		n.418-33538G>T		intron	N/A
	PCAT1	ENST00000645463.1		n.855+106053C>A		intron	N/A
	PCAT1	ENST00000646670.1		n.1064+98897C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23857 AN: 152026 Hom.: 4275 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.157 AC: 23926 AN: 152144 Hom.: 4294 Cov.: 32 AF XY: 0.155 AC XY: 11508 AN XY: 74384

African (AFR) AF: 0.434 AC: 18008 AN: 41450

American (AMR) AF: 0.0683 AC: 1044 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1265 AN: 5178

South Asian (SAS) AF: 0.102 AC: 492 AN: 4824

European-Finnish (FIN) AF: 0.0507 AC: 537 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0322 AC: 2191 AN: 68018

Other (OTH) AF: 0.112 AC: 237 AN: 2108

Alfa AF: 0.0790 Hom.: 4178

Bravo AF: 0.170

Asia WGS AF: 0.146 AC: 508 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.21
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs16901979; hg19: chr8-128124916;