rs4777189

chr15-69751044-G-Achr15-69751044-G-C

Variant summary

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

The ENST00000687931.2(ENSG00000289525):n.255-2004C>T 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 0.526 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: ENST00000687931.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

(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=-0.91).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687931.2	n.255-2004C>T		intron_variant, non_coding_transcript_variant
DRAIC	ENST00000647319.1	n.916-1334G>A		intron_variant, non_coding_transcript_variant
	ENST00000686507.1	n.223-21C>T		intron_variant, non_coding_transcript_variant

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;