Genetic Variant ENST00000558941.6:n.464-124C>T (chr15-69695543-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000558941.6(DRAIC):n.464-124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,120 control chromosomes in the GnomAD database, including 31,063 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 0.64 ( 31056 hom., cov: 32)

Exomes 𝑓: 0.50 ( 7 hom. )

Consequence

DRAIC
ENST00000558941.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.68

Publications

9 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCAT29	NR_126437.1 link	n.611-124C>T		intron_variant	Intron 5 of 5
PCAT29	NR_126438.1 link	n.378-124C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DRAIC	ENST00000558941.6 link	n.464-124C>T	intron_variant	Intron 4 of 4	4
DRAIC	ENST00000559212.1 link	n.564-124C>T	intron_variant	Intron 4 of 4	3
DRAIC	ENST00000560655.5 link	n.365-124C>T	intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.637

AC:

96731

AN:

151950

Hom.:

31014

Cov.:

show subpopulations

Gnomad AFR

AF:

0.695

Gnomad AMI

AF:

0.828

Gnomad AMR

AF:

0.670

Gnomad ASJ

AF:

0.561

Gnomad EAS

AF:

0.783

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.587

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.649

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.393

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.563

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.389

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.646

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.637

AC:

96816

AN:

152068

Hom.:

31056

Cov.:

AF XY:

0.637

AC XY:

47335

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.695

AC:

28812

AN:

41454

American (AMR)

AF:

0.670

AC:

10237

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.561

AC:

1945

AN:

3470

East Asian (EAS)

AF:

0.784

AC:

4055

AN:

5172

South Asian (SAS)

AF:

0.570

AC:

2746

AN:

4816

European-Finnish (FIN)

AF:

0.587

AC:

6213

AN:

10584

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.596

AC:

40493

AN:

67968

Other (OTH)

AF:

0.646

AC:

1367

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1805

3610

5415

7220

9025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.627

Hom.:

10025

Bravo

AF:

0.651

Asia WGS

AF:

0.639

AC:

2221

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.068

(source)

DANN

Benign

0.36

PhyloP100

-2.7

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over