rs4508917

chr4-76024944-A-Gchr4-76024944-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000341029.9(ART3):c.-10+13624A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,018 control chromosomes in the GnomAD database, including 6,862 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 0.29 (6862 hom., cov: 32)
• Consequence: ART3 ENST00000341029.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

ART3 (HGNC:725): (ADP-ribosyltransferase 3 (inactive)) This gene encodes an arginine-specific ADP-ribosyltransferase. The encoded protein catalyzes a reversible reaction which modifies proteins by the addition or removal of ADP-ribose to an arginine residue to regulate the function of the modified protein. An ADP-ribosyltransferase pseudogene is located on chromosome 11. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ART3	NM_001130017.3	c.-10+13624A>G		intron_variant
ART3	NM_001377177.1	c.-10+13624A>G		intron_variant
ART3	NM_001377181.1	c.-10+13624A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ART3	ENST00000341029.9	c.-10+13624A>G		intron_variant		1		P2
ART3	ENST00000513122.5	c.-125+13624A>G		intron_variant		1
ART3	ENST00000513353.5	c.-44+13624A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44600 AN: 151900 Hom.: 6848 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.294 AC: 44631 AN: 152018 Hom.: 6862 Cov.: 32 AF XY: 0.298 AC XY: 22140 AN XY: 74290

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.321

Alfa AF: 0.297 Hom.: 6565

Bravo AF: 0.298

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.93
Dann	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4508917; hg19: chr4-76946097;