15-69726651-A-G

Variant names:

• chr15-69726651-A-G
• rs7176508
• ENST00000647319.1:n.915+10872A>G

Variant summary

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

The ENST00000647319.1(DRAIC):​n.915+10872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,058 control chromosomes in the GnomAD database, including 33,950 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 0.66 (33950 hom., cov: 32)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 50 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRAIC	ENST00000647319.1	n.915+10872A>G		intron_variant	Intron 7 of 11

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100844 AN: 151940 Hom.: 33905 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.664 AC: 100939 AN: 152058 Hom.: 33950 Cov.: 32 AF XY: 0.663 AC XY: 49310 AN XY: 74340

African (AFR) AF: 0.762 AC: 31622 AN: 41474

American (AMR) AF: 0.685 AC: 10463 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3468

East Asian (EAS) AF: 0.803 AC: 4146 AN: 5164

South Asian (SAS) AF: 0.596 AC: 2876 AN: 4822

European-Finnish (FIN) AF: 0.591 AC: 6245 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41226 AN: 67960

Other (OTH) AF: 0.671 AC: 1419 AN: 2116

Alfa AF: 0.631 Hom.: 134927

Bravo AF: 0.682

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7176508; hg19: chr15-70018990;