Genetic Variant DRAIC:n.722-602T>C (chr15-69714984-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000647319.1(DRAIC):n.722-602T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,160 control chromosomes in the GnomAD database, including 32,892 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 ( 32892 hom., cov: 32)

Consequence

DRAIC
ENST00000647319.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39

Publications

10 publications found

Variant links:

Genes affected

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

DRAIC links:

ENSG00000303696 (HGNC:):

ENSG00000303696 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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 link	n.722-602T>C		intron_variant	Intron 6 of 11
ENSG00000303696	ENST00000796614.1 link	n.155-6294A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99410

AN:

152044

Hom.:

32849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.737

Gnomad AMI

AF:

0.828

Gnomad AMR

AF:

0.679

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.788

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.666

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

GnomAD4 genome

AF:

0.654

AC:

99497

AN:

152160

Hom.:

32892

Cov.:

AF XY:

0.653

AC XY:

48597

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.737

AC:

30607

AN:

41518

American (AMR)

AF:

0.679

AC:

10380

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.563

AC:

1954

AN:

3470

East Asian (EAS)

AF:

0.789

AC:

4087

AN:

5180

South Asian (SAS)

AF:

0.592

AC:

2854

AN:

4820

European-Finnish (FIN)

AF:

0.590

AC:

6240

AN:

10580

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.603

AC:

41014

AN:

67978

Other (OTH)

AF:

0.666

AC:

1407

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1768

3536

5304

7072

8840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.623

Hom.:

21423

Bravo

AF:

0.670

Asia WGS

AF:

0.673

AC:

2342

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.23

(source)

DANN

Benign

0.37

PhyloP100

-1.4

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over