rs6981122

Variant names:

• chr8-127082215-A-C
• rs6981122
• ENST00000523510.1:n.7T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-127082215-A-C
• chr8-127082215-A-T

Variant summary

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

The ENST00000523510.1(CASC19):​n.7T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,950 control chromosomes in the GnomAD database, including 26,369 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 0.58 (26369 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CASC19 ENST00000523510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 6 publications found

Genes affected

CASC19 (HGNC:49476): (cancer susceptibility 19)

PRNCR1 (HGNC:48942): (prostate cancer associated non-coding RNA 1)

PCAT2 (HGNC:45089): (prostate cancer associated transcript 2)

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.2342A>C		non_coding_transcript_exon_variant	Exon 1 of 1
PCAT2	NR_119373.1	n.7T>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000523510.1	n.7T>G		non_coding_transcript_exon_variant	Exon 1 of 4	3
PRNCR1	ENST00000635449.1	n.2342A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000641794.1	n.68T>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88249 AN: 151832 Hom.: 26345 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.567

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.581 AC: 88318 AN: 151950 Hom.: 26369 Cov.: 32 AF XY: 0.570 AC XY: 42305 AN XY: 74262

African (AFR) AF: 0.689 AC: 28530 AN: 41426

American (AMR) AF: 0.430 AC: 6556 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3271 AN: 5166

South Asian (SAS) AF: 0.386 AC: 1859 AN: 4822

European-Finnish (FIN) AF: 0.556 AC: 5877 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38788 AN: 67932

Other (OTH) AF: 0.568 AC: 1199 AN: 2112

Alfa AF: 0.562 Hom.: 31285

Bravo AF: 0.583

Asia WGS AF: 0.502 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.30
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6981122; hg19: chr8-128094460;