dbSNP rs3088189: ART4:p.Leu208Leu (chr12-14840674-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_021071.4(ART4):c.624C>T(p.Leu208Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,613,800 control chromosomes in the GnomAD database, including 116,040 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.34 ( 9314 hom., cov: 32)

Exomes 𝑓: 0.38 ( 106726 hom. )

Consequence

ART4
NM_021071.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.267

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 12-14840674-G-A is Benign according to our data. Variant chr12-14840674-G-A is described in ClinVar as [Benign]. Clinvar id is 3059324.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.267 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART4	NM_021071.4 link	c.624C>T	p.Leu208Leu	synonymous_variant	Exon 2 of 3	ENST00000228936.6	NP_066549.2	Q93070
ART4	NM_001354646.2 link	c.624C>T	p.Leu208Leu	synonymous_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.624C>T	p.Leu208Leu	synonymous_variant	Exon 2 of 3	1	NM_021071.4	ENSP00000228936.4		Q93070

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51590

AN:

151922

Hom.:

9299

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:

0.0993

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.354

GnomAD3 exomes

AF:

0.347

AC:

87145

AN:

250944

Hom.:

16004

AF XY:

0.356

AC XY:

48291

AN XY:

135606

show subpopulations

Gnomad AFR exome

AF:

0.276

Gnomad AMR exome

AF:

0.354

Gnomad ASJ exome

AF:

0.358

Gnomad EAS exome

AF:

0.0978

Gnomad SAS exome

AF:

0.396

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.390

Gnomad OTH exome

AF:

0.367

GnomAD4 exome

AF:

0.377

AC:

550984

AN:

1461760

Hom.:

106726

Cov.:

AF XY:

0.378

AC XY:

275199

AN XY:

727168

show subpopulations

Gnomad4 AFR exome

AF:

0.274

Gnomad4 AMR exome

AF:

0.352

Gnomad4 ASJ exome

AF:

0.362

Gnomad4 EAS exome

AF:

0.102

Gnomad4 SAS exome

AF:

0.394

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.394

Gnomad4 OTH exome

AF:

0.360

GnomAD4 genome

AF:

0.339

AC:

51616

AN:

152040

Hom.:

9314

Cov.:

AF XY:

0.336

AC XY:

24972

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.375

Gnomad4 ASJ

AF:

0.372

Gnomad4 EAS

AF:

0.0989

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.299

Gnomad4 NFE

AF:

0.386

Gnomad4 OTH

AF:

0.356

Alfa

AF:

0.380

Hom.:

21928

Bravo

AF:

0.341

Asia WGS

AF:

0.244

AC:

853

AN:

3478

EpiCase

AF:

0.395

EpiControl

AF:

0.404

ClinVar

Significance: Benign

Submissions summary: Benign: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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.1

DANN

Benign

0.83

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over