15-69751044-G-A

Variant names:

• chr15-69751044-G-A
• rs4777189
• ENST00000647319.1:n.916-1334G>A

Variant summary

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

The ENST00000647319.1(DRAIC):​n.916-1334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,978 control chromosomes in the GnomAD database, including 21,520 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 0.53 (21520 hom., cov: 32)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 9 publications found

Genes affected

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

ENSG00000289525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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.916-1334G>A		intron	N/A
	ENSG00000289525	ENST00000686507.2		n.261-21C>T		intron	N/A
	ENSG00000289525	ENST00000687931.3		n.261-2004C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79894 AN: 151860 Hom.: 21481 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.526 AC: 79979 AN: 151978 Hom.: 21520 Cov.: 32 AF XY: 0.527 AC XY: 39113 AN XY: 74254

African (AFR) AF: 0.605 AC: 25080 AN: 41440

American (AMR) AF: 0.591 AC: 9012 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3472

East Asian (EAS) AF: 0.748 AC: 3860 AN: 5162

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4939 AN: 10550

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31602 AN: 67960

Other (OTH) AF: 0.549 AC: 1158 AN: 2110

Alfa AF: 0.490 Hom.: 78645

Bravo AF: 0.550

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.097
DANN	Benign	0.18
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4777189; hg19: chr15-70043383;