Variant 15-69643743-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000560655.5(DRAIC):n.102-27997A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,092 control chromosomes in the GnomAD database, including 10,966 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 0.37 ( 10966 hom., cov: 32)

Consequence

DRAIC
ENST00000560655.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.334

Variant links:

Genes affected

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

DRAIC links:

PCAT29 (HGNC:50895): (prostate cancer associated transcript 29) This gene is thought to produce a functional long non-coding RNA. This transcript was identified in prostate cancer cells and may suppress tumor formation. [provided by RefSeq, Feb 2015]

PCAT29 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCAT29	NR_126437.1 link	n.369+14871A>G		intron_variant
PCAT29	NR_126438.1 link	n.115-27997A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
DRAIC	ENST00000560655.5 link	n.102-27997A>G	intron_variant	3
DRAIC	ENST00000644274.2 link	n.1099-27983A>G	intron_variant
DRAIC	ENST00000645479.2 link	n.1511+14871A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55687

AN:

151974

Hom.:

10958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.337

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.430

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.826

Gnomad SAS

AF:

0.482

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.344

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

GnomAD4 genome

AF:

0.366

AC:

55740

AN:

152092

Hom.:

10966

Cov.:

AF XY:

0.376

AC XY:

27922

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.337

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.826

Gnomad4 SAS

AF:

0.483

Gnomad4 FIN

AF:

0.388

Gnomad4 NFE

AF:

0.326

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.319

Hom.:

7888

Bravo

AF:

0.372

Asia WGS

AF:

0.596

AC:

2076

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.9

DANN

Benign

0.80

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