Genetic Variant ENST00000558941.6:n.4572T>C (chr15-69699775-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000558941.6(DRAIC):n.4572T>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 0.653 in 152,126 control chromosomes in the GnomAD database, including 32,708 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 0.65 ( 32705 hom., cov: 32)

Exomes 𝑓: 0.60 ( 3 hom. )

Consequence

DRAIC
ENST00000558941.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Variant links:

Genes affected

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

DRAIC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 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	ENST00000558941.6 link	n.4572T>C		non_coding_transcript_exon_variant	Exon 5 of 5	4
DRAIC	ENST00000647319.1 link	n.649-38T>C		intron_variant	Intron 5 of 11

Frequencies

GnomAD3 genomes

AF:

0.653

AC:

99225

AN:

151988

Hom.:

32661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.718

Gnomad AMI

AF:

0.850

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.580

Gnomad EAS

AF:

0.802

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.591

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.609

Gnomad OTH

AF:

0.665

GnomAD4 exome

AF:

0.600

AC:

AN:

Hom.:

Cov.:

AF XY:

0.571

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.571

GnomAD4 genome

AF:

0.653

AC:

99314

AN:

152106

Hom.:

32705

Cov.:

AF XY:

0.653

AC XY:

48549

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.718

Gnomad4 AMR

AF:

0.683

Gnomad4 ASJ

AF:

0.580

Gnomad4 EAS

AF:

0.803

Gnomad4 SAS

AF:

0.595

Gnomad4 FIN

AF:

0.591

Gnomad4 NFE

AF:

0.609

Gnomad4 OTH

AF:

0.664

Alfa

AF:

0.637

Hom.:

11308

Bravo

AF:

0.669

Asia WGS

AF:

0.667

AC:

2320

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.31

DANN

Benign

0.18

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over