Genetic Variant ART5:p.Thr284Lys (chr11-3638763-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_053017.5(ART5):c.851C>A(p.Thr284Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,613,802 control chromosomes in the GnomAD database, including 42,223 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 8394 hom., cov: 31)

Exomes 𝑓: 0.21 ( 33829 hom. )

Consequence

ART5
NM_053017.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.778

Variant links:

Genes affected

ART5 (HGNC:24049): (ADP-ribosyltransferase 5) The protein encoded by this gene belongs to the ARG-specific ADP-ribosyltransferase family. Proteins in this family regulate the function of target proteins by attaching ADP-ribose to specific amino acid residues in their target proteins. The mouse homolog lacks a glycosylphosphatidylinositol-anchor signal sequence and is predicted to be a secretory enzyme. Several transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

ART5 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 (MetaRNN=9.080657E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART5	NM_053017.5 link	c.851C>A	p.Thr284Lys	missense_variant	Exon 4 of 4	ENST00000397068.8	NP_443750.2	Q96L15-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART5	ENST00000397068.8 link	c.851C>A	p.Thr284Lys	missense_variant	Exon 4 of 4	1	NM_053017.5	ENSP00000380258.3		Q96L15-1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44724

AN:

151842

Hom.:

8364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.218

AC:

54792

AN:

251422

Hom.:

6995

AF XY:

0.211

AC XY:

28618

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.544

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.188

Gnomad EAS exome

AF:

0.240

Gnomad SAS exome

AF:

0.191

Gnomad FIN exome

AF:

0.183

Gnomad NFE exome

AF:

0.194

Gnomad OTH exome

AF:

0.197

GnomAD4 exome

AF:

0.207

AC:

302327

AN:

1461844

Hom.:

33829

Cov.:

AF XY:

0.206

AC XY:

149468

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.554

Gnomad4 AMR exome

AF:

0.189

Gnomad4 ASJ exome

AF:

0.187

Gnomad4 EAS exome

AF:

0.262

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.181

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.295

AC:

44810

AN:

151958

Hom.:

8394

Cov.:

AF XY:

0.292

AC XY:

21683

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.542

Gnomad4 AMR

AF:

0.218

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.191

Gnomad4 NFE

AF:

0.200

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.201

Hom.:

8147

Bravo

AF:

0.309

TwinsUK

AF:

0.196

AC:

726

ALSPAC

AF:

0.203

AC:

782

ESP6500AA

AF:

0.525

AC:

2312

ESP6500EA

AF:

0.198

AC:

1698

ExAC

AF:

0.224

AC:

27155

Asia WGS

AF:

0.225

AC:

781

AN:

3478

EpiCase

AF:

0.192

EpiControl

AF:

0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

6.9

DANN

Benign

0.60

DEOGEN2

Benign

0.011

T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.00022

LIST_S2

Benign

0.23

.;T

MetaRNN

Benign

0.000091

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-1.5

N;N

PrimateAI

Benign

0.40

PROVEAN

Benign

-0.10

N;N

REVEL

Benign

0.051

Sift

Benign

0.39

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.036

MPC

0.048

ClinPred

0.0056

GERP RS

2.8

Varity_R

0.030

gMVP

0.24

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