rs6836703

Variant names:

• chr4-76108994-G-A
• rs6836703
• NM_001130016.3:c.1036+1201G>A

Variant summary

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

The NM_001130016.3(ART3):​c.1036+1201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,042 control chromosomes in the GnomAD database, including 2,522 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 0.17 (2522 hom., cov: 32)
• Consequence: ART3 NM_001130016.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

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]

NUP54 (HGNC:17359): (nucleoporin 54) The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART3	NM_001130016.3	c.1036+1201G>A		intron_variant	Intron 11 of 11	ENST00000355810.9	NP_001123488.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART3	ENST00000355810.9	c.1036+1201G>A		intron_variant	Intron 11 of 11	1	NM_001130016.3	ENSP00000348064.4

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26425 AN: 151924 Hom.: 2513 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.174 AC: 26464 AN: 152042 Hom.: 2522 Cov.: 32 AF XY: 0.173 AC XY: 12829 AN XY: 74322

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.169

Alfa AF: 0.158 Hom.: 3075

Bravo AF: 0.178

Asia WGS AF: 0.247 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs6836703; hg19: chr4-77030147;