15-69712013-G-C

Variant names:

• chr15-69712013-G-C
• rs3902140
• ENST00000647319.1:n.722-3573G>C

Variant summary

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

The ENST00000647319.1(DRAIC):​n.722-3573G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,036 control chromosomes in the GnomAD database, including 32,836 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 0.65 (32836 hom., cov: 32)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 9 publications found

Genes affected

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

ENSG00000303696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647319.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRAIC	ENST00000647319.1		n.722-3573G>C		intron	N/A
	ENSG00000303696	ENST00000796614.1		n.155-3323C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99285 AN: 151916 Hom.: 32790 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.654 AC: 99377 AN: 152036 Hom.: 32836 Cov.: 32 AF XY: 0.653 AC XY: 48509 AN XY: 74298

African (AFR) AF: 0.742 AC: 30775 AN: 41478

American (AMR) AF: 0.678 AC: 10376 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1949 AN: 3472

East Asian (EAS) AF: 0.783 AC: 4042 AN: 5164

South Asian (SAS) AF: 0.584 AC: 2812 AN: 4814

European-Finnish (FIN) AF: 0.590 AC: 6226 AN: 10548

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40847 AN: 67952

Other (OTH) AF: 0.665 AC: 1398 AN: 2102

Alfa AF: 0.470 Hom.: 1149

Bravo AF: 0.670

Asia WGS AF: 0.659 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.79

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: rs3902140;

hg19: chr15-70004352;