rs8026898

chr15-69699078-G-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRAIC	ENST00000558941.6	n.3875G>A		non_coding_transcript_exon_variant	5/5	4
DRAIC	ENST00000647319.1	n.648+548G>A		intron_variant, non_coding_transcript_variant

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;