rs8026898

Variant names:

• chr15-69699078-G-A
• rs8026898
• ENST00000558941.6:n.3875G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558941.6(DRAIC):​n.3875G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,018 control chromosomes in the GnomAD database, including 10,024 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 0.34 (10024 hom., cov: 31)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: DRAIC ENST00000558941.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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	ENST00000558941.6	n.3875G>A		non_coding_transcript_exon_variant	Exon 5 of 5	4
DRAIC	ENST00000647319.1	n.648+548G>A		intron_variant	Intron 5 of 11

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51700 AN: 151830 Hom.: 9984 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.321

GnomAD4 exome AF: 0.143 AC: 10 AN: 70 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 8 AN XY: 48

Gnomad4 AFR exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.175

GnomAD4 genome AF: 0.341 AC: 51799 AN: 151948 Hom.: 10024 Cov.: 31 AF XY: 0.339 AC XY: 25149 AN XY: 74268

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0958

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.321

Alfa AF: 0.287 Hom.: 3716

Bravo AF: 0.349

Asia WGS AF: 0.226 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8026898; hg19: chr15-69991417;