rs56061981

Positions:

• chr4-76023632-C-T

Variant summary

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

The ENST00000341029.9(ART3):​c.-10+12312C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0672 in 491,938 control chromosomes in the GnomAD database, including 1,535 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 0.076 (551 hom., cov: 32)
  • Exomes 𝑓: 0.063 (984 hom.)
• Consequence: ART3 ENST00000341029.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ART3	NM_001130017.3	c.-10+12312C>T		intron_variant			NP_001123489.1
ART3	NM_001377177.1	c.-10+12312C>T		intron_variant			NP_001364106.1
ART3	NM_001377181.1	c.-10+12312C>T		intron_variant			NP_001364110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ART3	ENST00000341029.9	c.-10+12312C>T		intron_variant		1		ENSP00000343843	P2
ART3	ENST00000513122.5	c.-125+12312C>T		intron_variant		1		ENSP00000422287
ART3	ENST00000513353.5	c.-44+12312C>T		intron_variant		1		ENSP00000421345

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11586 AN: 152046 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0989

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0885

GnomAD4 exome AF: 0.0631 AC: 21430 AN: 339774 Hom.: 984 AF XY: 0.0642 AC XY: 11272 AN XY: 175626

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.0972

Gnomad4 ASJ exome AF: 0.0628

Gnomad4 EAS exome AF: 0.117

Gnomad4 SAS exome AF: 0.130

Gnomad4 FIN exome AF: 0.0592

Gnomad4 NFE exome AF: 0.0427

Gnomad4 OTH exome AF: 0.0667

GnomAD4 genome AF: 0.0763 AC: 11611 AN: 152164 Hom.: 551 Cov.: 32 AF XY: 0.0787 AC XY: 5857 AN XY: 74392

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0915

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.0989

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0420

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0582 Hom.: 93

Bravo AF: 0.0802

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56061981; hg19: chr4-76944785;