Variant 6-41071106-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

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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_addAF=-0.818108).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OARD1	NM_001329686.2 linkuse as main transcript	c.184+26G>A		intron_variant		ENST00000424266.7	NP_001316615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OARD1	ENST00000424266.7 linkuse as main transcript	c.184+26G>A		intron_variant		2	NM_001329686.2	ENSP00000416829	P1

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

GnomAD3 exomes

AF:

0.272

AC:

68262

AN:

251250

Hom.:

10075

AF XY:

0.263

AC XY:

35723

AN XY:

135834

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 SAS exome

AF:

0.291

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

Gnomad4 AFR exome

AF:

0.459

Gnomad4 AMR exome

AF:

0.372

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.287

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.229

Gnomad4 OTH exome

AF:

0.246

GnomAD4 genome

AF:

0.302

AC:

45884

AN:

152094

Hom.:

7764

Cov.:

AF XY:

0.300

AC XY:

22282

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.450

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.256

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.237

Hom.:

3980

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.34

DANN

Benign

0.79

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.021

MutationTaster

Benign

3.1e-7

P;P;P;P;P;P;P;P;P;P;P;P

Vest4

0.073

GERP RS

-7.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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

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