NM_021071.4:c.793G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_021071.4(ART4):c.793G>A(p.Asp265Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,613,718 control chromosomes in the GnomAD database, including 116,052 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign,Affects (no stars).

Frequency

Genomes: 𝑓 0.34 ( 9319 hom., cov: 32)

Exomes 𝑓: 0.38 ( 106733 hom. )

Consequence

ART4
NM_021071.4 missense

Scores

Clinical Significance

Benign; Affects no assertion criteria provided B:1O:1

Conservation

PhyloP100: 0.304

Publications

58 publications found

Variant links:

Genes affected

ART4 (HGNC:726): (ADP-ribosyltransferase 4 (inactive) (Dombrock blood group)) This gene encodes a protein that contains a mono-ADP-ribosylation (ART) motif. It is a member of the ADP-ribosyltransferase gene family but enzymatic activity has not been demonstrated experimentally. Antigens of the Dombrock blood group system are located on the gene product, which is glycosylphosphatidylinosotol-anchored to the erythrocyte membrane. Allelic variants, some of which lead to adverse transfusion reactions, are known. [provided by RefSeq, Jul 2008]

ART4 links:

C12orf60 (HGNC:28726): (chromosome 12 open reading frame 60)

C12orf60 links:

ENSG00000256339 (HGNC:):

ENSG00000256339 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0048785806).

BP6

Variant 12-14840505-C-T is Benign according to our data. Variant chr12-14840505-C-T is described in ClinVar as Benign|Affects. ClinVar VariationId is 17730.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART4	NM_021071.4 link	c.793G>A	p.Asp265Asn	missense_variant	Exon 2 of 3	ENST00000228936.6	NP_066549.2
ART4	NM_001354646.2 link	c.793G>A	p.Asp265Asn	missense_variant	Exon 2 of 2		NP_001341575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART4	ENST00000228936.6 link	c.793G>A	p.Asp265Asn	missense_variant	Exon 2 of 3	1	NM_021071.4	ENSP00000228936.4

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51617

AN:

151986

Hom.:

9304

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.524

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.372

Gnomad EAS

AF:

0.0990

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.354

GnomAD2 exomes

AF:

0.347

AC:

87154

AN:

250948

AF XY:

0.356

show subpopulations

Gnomad AFR exome

AF:

0.275

Gnomad AMR exome

AF:

0.354

Gnomad ASJ exome

AF:

0.358

Gnomad EAS exome

AF:

0.0977

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.391

Gnomad OTH exome

AF:

0.367

GnomAD4 exome

AF:

0.377

AC:

550919

AN:

1461614

Hom.:

106733

Cov.:

AF XY:

0.378

AC XY:

275167

AN XY:

727100

show subpopulations

African (AFR)

AF:

0.274

AC:

9163

AN:

33478

American (AMR)

AF:

0.352

AC:

15731

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

9451

AN:

26120

East Asian (EAS)

AF:

0.102

AC:

4067

AN:

39700

South Asian (SAS)

AF:

0.394

AC:

34002

AN:

86194

European-Finnish (FIN)

AF:

0.301

AC:

16092

AN:

53416

Middle Eastern (MID)

AF:

0.442

AC:

2543

AN:

5758

European-Non Finnish (NFE)

AF:

0.394

AC:

438110

AN:

1111866

Other (OTH)

AF:

0.360

AC:

21760

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

18752

37505

56257

75010

93762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13568

27136

40704

54272

67840

<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:

0.340

AC:

51642

AN:

152104

Hom.:

9319

Cov.:

AF XY:

0.336

AC XY:

25000

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.277

AC:

11483

AN:

41478

American (AMR)

AF:

0.374

AC:

5727

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.372

AC:

1289

AN:

3466

East Asian (EAS)

AF:

0.0987

AC:

511

AN:

5178

South Asian (SAS)

AF:

0.384

AC:

1853

AN:

4826

European-Finnish (FIN)

AF:

0.300

AC:

3168

AN:

10574

Middle Eastern (MID)

AF:

0.397

AC:

116

AN:

292

European-Non Finnish (NFE)

AF:

0.386

AC:

26269

AN:

67978

Other (OTH)

AF:

0.356

AC:

751

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1693

3387

5080

6774

8467

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<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:

0.368

Hom.:

26891

Bravo

AF:

0.341

TwinsUK

AF:

0.394

AC:

1461

ALSPAC

AF:

0.403

AC:

1554

ESP6500AA

AF:

0.279

AC:

1230

ESP6500EA

AF:

0.395

AC:

3400

ExAC

AF:

0.348

AC:

42316

Asia WGS

AF:

0.244

AC:

853

AN:

3478

EpiCase

AF:

0.395

EpiControl

AF:

0.403

ClinVar

Significance: Benign; Affects

Submissions summary: Benign:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ART4-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Blood group, Dombrock system

Other:1

Oct 01, 2000

OMIM

Significance:Affects

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.8

(source)

DANN

Benign

0.54

DEOGEN2

Benign

0.00058

.;T

Eigen

Benign

-0.95

Eigen_PC

Benign

-0.89

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.17

.;T

MetaRNN

Benign

0.0049

T;T

MetaSVM

Benign

-0.93

PhyloP100

0.30

PrimateAI

Benign

0.36

PROVEAN

Benign

2.1

N;N

REVEL

Benign

0.046

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Vest4

0.023

MPC

0.0097

ClinPred

0.0029

GERP RS

1.1

gMVP

0.26

Mutation Taster

=99/1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over