Genetic Variant OARD1:c.184+26G>A (chr6-41071106-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 NM_001329686.2(OARD1):c.184+26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,610,832 control chromosomes in the GnomAD database, including 52,594 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 0.30 ( 7764 hom., cov: 33)

Exomes 𝑓: 0.24 ( 44830 hom. )

Consequence

OARD1
NM_001329686.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

13 publications found

Variant links:

Genes affected

OARD1 (HGNC:21257): (O-acyl-ADP-ribose deacylase 1) The protein encoded by this gene is a deacylase that can convert O-acetyl-ADP-ribose to ADP-ribose and acetate, O-propionyl-ADP-ribose to ADP-ribose and propionate, and O-butyryl-ADP-ribose to ADP-ribose and butyrate. The ADP-ribose product is able to inhibit these reactions through a competitive feedback loop. [provided by RefSeq, Jul 2016]

OARD1 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_addAF=-0.818108).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329686.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OARD1	NM_001329686.2	MANE Select	c.184+26G>A	intron	N/A	NP_001316615.1	Q9Y530
OARD1	NM_001329684.2		c.184+26G>A	intron	N/A	NP_001316613.1	Q9Y530
OARD1	NM_001329685.1		c.184+26G>A	intron	N/A	NP_001316614.1	Q9Y530

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OARD1	ENST00000424266.7	TSL:2 MANE Select	c.184+26G>A	intron	N/A	ENSP00000416829.2	Q9Y530
OARD1	ENST00000479950.5	TSL:1	c.184+26G>A	intron	N/A	ENSP00000420484.1	Q9Y530
OARD1	ENST00000373154.6	TSL:1	c.184+26G>A	intron	N/A	ENSP00000362247.2	C9J5P1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45833

AN:

151976

Hom.:

7753

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.272

GnomAD2 exomes

AF:

0.272

AC:

68262

AN:

251250

AF XY:

0.263

show subpopulations

Gnomad AFR exome

AF:

0.457

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.194

Gnomad EAS exome

AF:

0.254

Gnomad FIN exome

AF:

0.231

Gnomad NFE exome

AF:

0.227

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.243

AC:

354324

AN:

1458738

Hom.:

44830

Cov.:

AF XY:

0.242

AC XY:

176013

AN XY:

725914

show subpopulations

African (AFR)

AF:

0.459

AC:

15311

AN:

33392

American (AMR)

AF:

0.372

AC:

16615

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

5102

AN:

26106

East Asian (EAS)

AF:

0.249

AC:

9862

AN:

39682

South Asian (SAS)

AF:

0.287

AC:

24715

AN:

86192

European-Finnish (FIN)

AF:

0.231

AC:

12332

AN:

53406

Middle Eastern (MID)

AF:

0.252

AC:

1449

AN:

5756

European-Non Finnish (NFE)

AF:

0.229

AC:

254136

AN:

1109202

Other (OTH)

AF:

0.246

AC:

14802

AN:

60280

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

13091

26181

39272

52362

65453

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8904

17808

26712

35616

44520

<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:

0.302

AC:

45884

AN:

152094

Hom.:

7764

Cov.:

AF XY:

0.300

AC XY:

22282

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.450

AC:

18643

AN:

41440

American (AMR)

AF:

0.315

AC:

4807

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.200

AC:

692

AN:

3468

East Asian (EAS)

AF:

0.256

AC:

1327

AN:

5178

South Asian (SAS)

AF:

0.289

AC:

1397

AN:

4832

European-Finnish (FIN)

AF:

0.230

AC:

2432

AN:

10584

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15778

AN:

67992

Other (OTH)

AF:

0.268

AC:

567

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1612

3224

4837

6449

8061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.263

Hom.:

9099

Bravo

AF:

0.312

TwinsUK

AF:

0.233

AC:

863

ALSPAC

AF:

0.220

AC:

849

ESP6500AA

AF:

0.450

AC:

1982

ESP6500EA

AF:

0.231

AC:

1987

ExAC

AF:

0.272

AC:

33052

Asia WGS

AF:

0.312

AC:

1084

AN:

3478

EpiCase

AF:

0.220

EpiControl

AF:

0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.34

(source)

DANN

Benign

0.79

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.021

PhyloP100

-1.8

Vest4

0.073

GERP RS

-7.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Mutation Taster

=189/11

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over