rs10518826

Variant names:

• chr15-69680619-C-T
• rs10518826
• ENST00000558941.6:n.317+2979C>T

Variant summary

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

The ENST00000558941.6(DRAIC):​n.317+2979C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,020 control chromosomes in the GnomAD database, including 36,657 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 0.69 (36657 hom., cov: 31)
• Consequence: DRAIC ENST00000558941.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 3 publications found

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

PCAT29 (HGNC:50895): (prostate cancer associated transcript 29) This gene is thought to produce a functional long non-coding RNA. This transcript was identified in prostate cancer cells and may suppress tumor formation. [provided by RefSeq, Feb 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCAT29	NR_126437.1	n.464+2979C>T		intron_variant	Intron 4 of 5
PCAT29	NR_126438.1	n.377+2979C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRAIC	ENST00000558941.6	n.317+2979C>T		intron_variant	Intron 3 of 4	4
DRAIC	ENST00000559212.1	n.256-528C>T		intron_variant	Intron 2 of 4	3
DRAIC	ENST00000560655.5	n.364+2979C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104926 AN: 151902 Hom.: 36630 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.691 AC: 104996 AN: 152020 Hom.: 36657 Cov.: 31 AF XY: 0.692 AC XY: 51381 AN XY: 74290

African (AFR) AF: 0.791 AC: 32834 AN: 41502

American (AMR) AF: 0.710 AC: 10841 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2028 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3783 AN: 5152

South Asian (SAS) AF: 0.637 AC: 3065 AN: 4812

European-Finnish (FIN) AF: 0.659 AC: 6958 AN: 10554

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43013 AN: 67940

Other (OTH) AF: 0.711 AC: 1501 AN: 2112

Alfa AF: 0.664 Hom.: 22064

Bravo AF: 0.704

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.17
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10518826; hg19: chr15-69972958;