rs867562

Positions:

• chr4-76013587-G-A
• chr4-76013587-G-C

Variant summary

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

The ENST00000341029.9(ART3):​c.-10+2267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,132 control chromosomes in the GnomAD database, including 2,041 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 0.14 (2041 hom., cov: 32)
• Consequence: ART3 ENST00000341029.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ART3	NM_001130017.3	c.-10+2267G>A		intron_variant			NP_001123489.1
ART3	NM_001377177.1	c.-10+2267G>A		intron_variant			NP_001364106.1
ART3	NM_001377181.1	c.-10+2267G>A		intron_variant			NP_001364110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ART3	ENST00000341029.9	c.-10+2267G>A		intron_variant		1		ENSP00000343843	P2
ART3	ENST00000513122.5	c.-125+2267G>A		intron_variant		1		ENSP00000422287
ART3	ENST00000513353.5	c.-44+2267G>A		intron_variant		1		ENSP00000421345

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21632 AN: 152012 Hom.: 2041 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.142 AC: 21636 AN: 152132 Hom.: 2041 Cov.: 32 AF XY: 0.142 AC XY: 10541 AN XY: 74368

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.151

Alfa AF: 0.147 Hom.: 249

Bravo AF: 0.143

Asia WGS AF: 0.242 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867562; hg19: chr4-76934740;