rs10152591

Positions:

• chr15-69755818-A-C

Variant summary

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

The XR_001751592.3(LOC107984788):​n.569-338A>C 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 0.0955 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: LOC107984788 XR_001751592.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LOC107984788 (HGNC:):

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=-0.75).
• 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/exons	MANE	UniProt
LOC107984788	XR_001751592.3	n.569-338A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRAIC	ENST00000647319.1	n.1055-338A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0528

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.0950

Gnomad4 FIN AF: 0.0614

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0918 Hom.: 785

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10152591; hg19: chr15-70048157;