chr15-69714534-G-A

Variant names:

• chr15-69714534-G-A
• rs4776472
• ENST00000647319.1:n.722-1052G>A

Variant summary

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

The ENST00000647319.1(DRAIC):​n.722-1052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,752 control chromosomes in the GnomAD database, including 4,607 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 0.21 (4607 hom., cov: 31)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825
• Publications: 19 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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.722-1052G>A		intron	N/A
	ENSG00000303696	ENST00000796614.1		n.155-5844C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32336 AN: 151634 Hom.: 4612 Cov.: 31

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.213 AC: 32321 AN: 151752 Hom.: 4607 Cov.: 31 AF XY: 0.219 AC XY: 16211 AN XY: 74164

African (AFR) AF: 0.0845 AC: 3493 AN: 41344

American (AMR) AF: 0.339 AC: 5169 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3518 AN: 5116

South Asian (SAS) AF: 0.191 AC: 918 AN: 4796

European-Finnish (FIN) AF: 0.246 AC: 2603 AN: 10564

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15161 AN: 67900

Other (OTH) AF: 0.260 AC: 547 AN: 2104

Alfa AF: 0.232 Hom.: 14613

Bravo AF: 0.223

Asia WGS AF: 0.374 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.82
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs4776472; hg19: chr15-70006873;