chr11-3664425-A-G

Variant names:

• chr11-3664425-A-G
• rs2271583
• NM_004314.3:c.*236A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004314.3(ART1):​c.*236A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 467,980 control chromosomes in the GnomAD database, including 158,810 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 0.82 (50726 hom., cov: 29)
  • Exomes 𝑓: 0.83 (108084 hom.)
• Consequence: ART1 NM_004314.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 6 publications found

Genes affected

ART1 (HGNC:723): (ADP-ribosyltransferase 1) ADP-ribosyltransferase catalyzes the ADP-ribosylation of arginine residues in proteins. Mono-ADP-ribosylation is a posttranslational modification of proteins that is interfered with by a variety of bacterial toxins including cholera, pertussis, and heat-labile enterotoxins of E. coli. The amino acid sequence consists of predominantly hydrophobic N- and C-terminal regions, which is characteristic of glycosylphosphatidylinositol (GPI)-anchored proteins. This gene was previously designated ART2. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART1	NM_004314.3	c.*236A>G		downstream_gene_variant		ENST00000250693.2	NP_004305.2
ART1	XM_011520114.4	c.*236A>G		downstream_gene_variant			XP_011518416.1
ART1	XM_017017763.3	c.*236A>G		downstream_gene_variant			XP_016873252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART1	ENST00000250693.2	c.*236A>G		downstream_gene_variant		1	NM_004314.3	ENSP00000250693.1

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123786 AN: 151820 Hom.: 50693 Cov.: 29

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.838

GnomAD4 exome AF: 0.826 AC: 260954 AN: 316042 Hom.: 108084 Cov.: 3 AF XY: 0.826 AC XY: 137624 AN XY: 166654

African (AFR) AF: 0.784 AC: 6810 AN: 8686

American (AMR) AF: 0.926 AC: 11833 AN: 12784

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 8701 AN: 9644

East Asian (EAS) AF: 0.754 AC: 15346 AN: 20348

South Asian (SAS) AF: 0.817 AC: 27141 AN: 33220

European-Finnish (FIN) AF: 0.752 AC: 15264 AN: 20300

Middle Eastern (MID) AF: 0.870 AC: 1222 AN: 1404

European-Non Finnish (NFE) AF: 0.833 AC: 159252 AN: 191180

Other (OTH) AF: 0.833 AC: 15385 AN: 18476

GnomAD4 genome AF: 0.815 AC: 123875 AN: 151938 Hom.: 50726 Cov.: 29 AF XY: 0.814 AC XY: 60421 AN XY: 74258

African (AFR) AF: 0.781 AC: 32339 AN: 41416

American (AMR) AF: 0.906 AC: 13836 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3143 AN: 3464

East Asian (EAS) AF: 0.739 AC: 3807 AN: 5154

South Asian (SAS) AF: 0.820 AC: 3931 AN: 4796

European-Finnish (FIN) AF: 0.722 AC: 7610 AN: 10544

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56385 AN: 67974

Other (OTH) AF: 0.836 AC: 1763 AN: 2110

Alfa AF: 0.835 Hom.: 96943

Bravo AF: 0.828

Asia WGS AF: 0.793 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		0.081
Mutation Taster		=79/21	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2271583; hg19: chr11-3685655;