15-69667454-C-G

Variant names:

• chr15-69667454-C-G
• rs892416
• ENST00000560655.5:n.102-4286C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000560655.5(DRAIC):​n.102-4286C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.011 (46 hom., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: DRAIC ENST00000560655.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT29	NR_126437.1		n.370-10092C>G		intron	N/A
	PCAT29	NR_126438.1		n.115-4286C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRAIC	ENST00000560655.5	TSL:3	n.102-4286C>G		intron	N/A
	DRAIC	ENST00000644274.2		n.1099-4272C>G		intron	N/A
	DRAIC	ENST00000645479.2		n.1512-4286C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0113 AC: 931 AN: 82030 Hom.: 45 Cov.: 17

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00354

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00287

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000131

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000344

Gnomad OTH AF: 0.0141

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0114 AC: 938 AN: 82126 Hom.: 46 Cov.: 17 AF XY: 0.0112 AC XY: 459 AN XY: 41062

African (AFR) AF: 0.0344 AC: 870 AN: 25324

American (AMR) AF: 0.00354 AC: 35 AN: 9898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1768

East Asian (EAS) AF: 0.00288 AC: 6 AN: 2086

South Asian (SAS) AF: 0.00 AC: 0 AN: 1772

European-Finnish (FIN) AF: 0.000131 AC: 1 AN: 7614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.000344 AC: 11 AN: 31964

Other (OTH) AF: 0.0139 AC: 15 AN: 1082

Alfa AF: 0.00 Hom.: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs892416;

hg19: chr15-69959793;