chr15-69699078-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 38 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558941.6. 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	ENST00000558941.6	TSL:4	n.3875G>A		non_coding_transcript_exon	Exon 5 of 5
	DRAIC	ENST00000647319.1		n.648+548G>A		intron	N/A

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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.0833 AC: 2 AN: 24

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.175 AC: 7 AN: 40

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.537 AC: 22216 AN: 41400

American (AMR) AF: 0.278 AC: 4245 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3468

East Asian (EAS) AF: 0.0958 AC: 495 AN: 5166

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4826

European-Finnish (FIN) AF: 0.279 AC: 2941 AN: 10542

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18125 AN: 67956

Other (OTH) AF: 0.321 AC: 679 AN: 2114

Alfa AF: 0.292 Hom.: 15647

Bravo AF: 0.349

Asia WGS AF: 0.226 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.54
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs8026898; hg19: chr15-69991417;