NM_001130016.3:c.1036+1201G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

NUP54 Gene-Disease associations (from GenCC):

• dystonia 37, early-onset, with striatal lesions

  Inheritance: Unknown, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130016.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ART3	NM_001130016.3	MANE Select	c.1036+1201G>A		intron	N/A	NP_001123488.1	Q13508-1
	ART3	NM_001377173.1		c.1069+1201G>A		intron	N/A	NP_001364102.1	H0Y8V6
	ART3	NM_001437636.1		c.971-2913G>A		intron	N/A	NP_001424565.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ART3	ENST00000355810.9	TSL:1 MANE Select	c.1036+1201G>A		intron	N/A	ENSP00000348064.4	Q13508-1
	ART3	ENST00000511188.2	TSL:1	c.1069+1201G>A		intron	N/A	ENSP00000422249.2	H0Y8V6
	ART3	ENST00000349321.7	TSL:1	c.1003+1201G>A		intron	N/A	ENSP00000304313.5	Q13508-3

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

African (AFR) AF: 0.207 AC: 8592 AN: 41462

American (AMR) AF: 0.151 AC: 2310 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2100 AN: 5160

South Asian (SAS) AF: 0.126 AC: 607 AN: 4814

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10588

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10161 AN: 67968

Other (OTH) AF: 0.169 AC: 357 AN: 2116

Alfa AF: 0.161 Hom.: 7154

Bravo AF: 0.178

Asia WGS AF: 0.247 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.40
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6836703; hg19: chr4-77030147;