11-3664425-A-G

Position:

• chr11-3664425-A-G

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

(HGNC:):

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.3664425A>G		intergenic_region
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/exons	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

Gnomad4 AFR exome AF: 0.784

Gnomad4 AMR exome AF: 0.926

Gnomad4 ASJ exome AF: 0.902

Gnomad4 EAS exome AF: 0.754

Gnomad4 SAS exome AF: 0.817

Gnomad4 FIN exome AF: 0.752

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.833

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

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.836

Alfa AF: 0.836 Hom.: 69312

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2271583; hg19: chr11-3685655;