chr15-69755818-A-C

Variant names:

• chr15-69755818-A-C
• rs10152591
• ENST00000798868.1:n.131A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000798868.1(DRAIC):​n.131A>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 0.0955 in 152,202 control chromosomes in the GnomAD database, including 788 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 0.096 (788 hom., cov: 32)
• Consequence: DRAIC ENST00000798868.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 40 publications found

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

ENSG00000289525 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984788	XR_001751592.3	n.569-338A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRAIC	ENST00000798868.1	n.131A>C		non_coding_transcript_exon_variant	Exon 1 of 3
DRAIC	ENST00000798871.1	n.78A>C		non_coding_transcript_exon_variant	Exon 1 of 4
DRAIC	ENST00000798872.1	n.53A>C		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14537 AN: 152084 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0953

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0955 AC: 14538 AN: 152202 Hom.: 788 Cov.: 32 AF XY: 0.0918 AC XY: 6830 AN XY: 74428

African (AFR) AF: 0.132 AC: 5486 AN: 41506

American (AMR) AF: 0.0528 AC: 808 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.0189 AC: 98 AN: 5180

South Asian (SAS) AF: 0.0950 AC: 458 AN: 4822

European-Finnish (FIN) AF: 0.0614 AC: 651 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6665 AN: 68010

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.0944 Hom.: 1974

Bravo AF: 0.0947

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs10152591; hg19: chr15-70048157;