rs892416

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-69667454-C-A
• chr15-69667454-C-G
• chr15-69667454-C-T

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>A 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 0.026 (148 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=-0.83).

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>A		intron	N/A
	PCAT29	NR_126438.1		n.115-4286C>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0265 AC: 2172 AN: 81988 Hom.: 149 Cov.: 17

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.0675

Gnomad AMR AF: 0.00881

Gnomad ASJ AF: 0.0209

Gnomad EAS AF: 0.00574

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.00381

Gnomad MID AF: 0.0333

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0253

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: 0.0265 AC: 2173 AN: 82084 Hom.: 148 Cov.: 17 AF XY: 0.0246 AC XY: 1008 AN XY: 41048

African (AFR) AF: 0.0498 AC: 1260 AN: 25296

American (AMR) AF: 0.00889 AC: 88 AN: 9896

Ashkenazi Jewish (ASJ) AF: 0.0209 AC: 37 AN: 1768

East Asian (EAS) AF: 0.00575 AC: 12 AN: 2086

South Asian (SAS) AF: 0.0780 AC: 138 AN: 1770

European-Finnish (FIN) AF: 0.00381 AC: 29 AN: 7614

Middle Eastern (MID) AF: 0.0275 AC: 6 AN: 218

European-Non Finnish (NFE) AF: 0.0172 AC: 549 AN: 31954

Other (OTH) AF: 0.0250 AC: 27 AN: 1082

Alfa AF: 0.00157 Hom.: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism

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;

COSMIC: COSV73740768;