15-69853419-G-A

Variant names:

• chr15-69853419-G-A
• rs305009
• ENST00000798881.1:n.366-1436G>A

Variant summary

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

The ENST00000798881.1(DRAIC):​n.366-1436G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,084 control chromosomes in the GnomAD database, including 3,948 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 0.23 (3948 hom., cov: 32)
• Consequence: DRAIC ENST00000798881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 9 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798881.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRAIC	ENST00000798881.1		n.366-1436G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34316 AN: 151964 Hom.: 3945 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.226 AC: 34344 AN: 152084 Hom.: 3948 Cov.: 32 AF XY: 0.226 AC XY: 16799 AN XY: 74332

African (AFR) AF: 0.268 AC: 11094 AN: 41470

American (AMR) AF: 0.162 AC: 2482 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3464

East Asian (EAS) AF: 0.311 AC: 1610 AN: 5172

South Asian (SAS) AF: 0.180 AC: 866 AN: 4820

European-Finnish (FIN) AF: 0.251 AC: 2654 AN: 10568

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14181 AN: 67976

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.210 Hom.: 11280

Bravo AF: 0.222

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.54
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs305009; hg19: chr15-70145758;