15-69643743-A-G

Variant names:

• chr15-69643743-A-G
• rs4777168
• ENST00000560655.5:n.102-27997A>G

Variant summary

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

The ENST00000560655.5(DRAIC):​n.102-27997A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,092 control chromosomes in the GnomAD database, including 10,966 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 0.37 (10966 hom., cov: 32)
• Consequence: DRAIC ENST00000560655.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 2 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560655.5. 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
	PCAT29	NR_126437.1		n.369+14871A>G		intron	N/A
	PCAT29	NR_126438.1		n.115-27997A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRAIC	ENST00000560655.5	TSL:3	n.102-27997A>G		intron	N/A
	DRAIC	ENST00000644274.2		n.1099-27983A>G		intron	N/A
	DRAIC	ENST00000645479.2		n.1511+14871A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55687 AN: 151974 Hom.: 10958 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.366 AC: 55740 AN: 152092 Hom.: 10966 Cov.: 32 AF XY: 0.376 AC XY: 27922 AN XY: 74334

African (AFR) AF: 0.337 AC: 13979 AN: 41470

American (AMR) AF: 0.430 AC: 6570 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4272 AN: 5170

South Asian (SAS) AF: 0.483 AC: 2328 AN: 4820

European-Finnish (FIN) AF: 0.388 AC: 4092 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22158 AN: 67998

Other (OTH) AF: 0.348 AC: 736 AN: 2116

Alfa AF: 0.336 Hom.: 23587

Bravo AF: 0.372

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.9
DANN	Benign	0.80
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs4777168; hg19: chr15-69936082;