rs4776472

chr15-69714534-G-A

Variant summary

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

The ENST00000647319.1(DRAIC):n.722-1052G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,752 control chromosomes in the GnomAD database, including 4,607 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 0.21 (4607 hom., cov: 31)
• Consequence: DRAIC ENST00000647319.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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	ENST00000647319.1	n.722-1052G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32336 AN: 151634 Hom.: 4612 Cov.: 31

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.213 AC: 32321 AN: 151752 Hom.: 4607 Cov.: 31 AF XY: 0.219 AC XY: 16211 AN XY: 74164

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.260

Alfa AF: 0.243 Hom.: 10010

Bravo AF: 0.223

Asia WGS AF: 0.374 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.3
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4776472; hg19: chr15-70006873;