15-69797459-C-T

Variant names:

• chr15-69797459-C-T
• rs305050
• ENST00000647319.1:n.1376+726C>T

Variant summary

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

The ENST00000647319.1(DRAIC):​n.1376+726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,244 control chromosomes in the GnomAD database, including 65,187 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 0.92 (65187 hom., cov: 32)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 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	ENST00000647319.1	n.1376+726C>T		intron_variant	Intron 11 of 11
DRAIC	ENST00000674201.1	n.150+726C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139977 AN: 152126 Hom.: 65148 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.975

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.920 AC: 140068 AN: 152244 Hom.: 65187 Cov.: 32 AF XY: 0.921 AC XY: 68555 AN XY: 74452

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.929

Alfa AF: 0.961 Hom.: 15599

Bravo AF: 0.908

Asia WGS AF: 0.856 AC: 2977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305050; hg19: chr15-70089798;