15-69699775-T-C

Position:

• chr15-69699775-T-C

Variant summary

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

The ENST00000558941.6(DRAIC):​n.4572T>C 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 0.653 in 152,126 control chromosomes in the GnomAD database, including 32,708 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 0.65 (32705 hom., cov: 32)
  • Exomes 𝑓: 0.60 (3 hom.)
• Consequence: DRAIC ENST00000558941.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.92).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRAIC	ENST00000558941.6	n.4572T>C		non_coding_transcript_exon_variant	5/5	4
DRAIC	ENST00000647319.1	n.649-38T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99225 AN: 151988 Hom.: 32661 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.665

GnomAD4 exome AF: 0.600 AC: 12 AN: 20 Hom.: 3 Cov.: 0 AF XY: 0.571 AC XY: 8 AN XY: 14

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.571

GnomAD4 genome AF: 0.653 AC: 99314 AN: 152106 Hom.: 32705 Cov.: 32 AF XY: 0.653 AC XY: 48549 AN XY: 74350

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.664

Alfa AF: 0.637 Hom.: 11308

Bravo AF: 0.669

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10220831; hg19: chr15-69992114;