15-69699775-T-C

Variant names:

• chr15-69699775-T-C
• rs10220831
• ENST00000558941.6:n.4572T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRAIC	ENST00000558941.6	n.4572T>C		non_coding_transcript_exon_variant	Exon 5 of 5	4
DRAIC	ENST00000647319.1	n.649-38T>C		intron_variant	Intron 5 of 11

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.571 AC: 8 AN: 14

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.718 AC: 29820 AN: 41516

American (AMR) AF: 0.683 AC: 10428 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3466

East Asian (EAS) AF: 0.803 AC: 4156 AN: 5178

South Asian (SAS) AF: 0.595 AC: 2865 AN: 4814

European-Finnish (FIN) AF: 0.591 AC: 6245 AN: 10562

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41413 AN: 67976

Other (OTH) AF: 0.664 AC: 1404 AN: 2114

Alfa AF: 0.637 Hom.: 13800

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10220831; hg19: chr15-69992114;