rs4777189

Variant names:

• chr15-69751044-G-A
• rs4777189
• ENST00000647319.1:n.916-1334G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-69751044-G-A
• chr15-69751044-G-C

Variant summary

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

The ENST00000647319.1(DRAIC):​n.916-1334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,978 control chromosomes in the GnomAD database, including 21,520 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 0.53 (21520 hom., cov: 32)
• Consequence: DRAIC ENST00000647319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

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

ENSG00000289525 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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.916-1334G>A		intron_variant	Intron 7 of 11
ENSG00000289525	ENST00000686507.1	n.223-21C>T		intron_variant	Intron 1 of 2
ENSG00000289525	ENST00000687931.2	n.255-2004C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79894 AN: 151860 Hom.: 21481 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.526 AC: 79979 AN: 151978 Hom.: 21520 Cov.: 32 AF XY: 0.527 AC XY: 39113 AN XY: 74254

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.549

Alfa AF: 0.483 Hom.: 36240

Bravo AF: 0.550

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.097
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4777189; hg19: chr15-70043383;