rs16925377

chr11-3655845-T-G

Variant summary

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

The NM_004314.3(ART1):c.-52-3317T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,924 control chromosomes in the GnomAD database, including 934 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 0.11 (934 hom., cov: 31)
• Consequence: ART1 NM_004314.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ART1	NM_004314.3	c.-52-3317T>G		intron_variant		ENST00000250693.2
ART1	XM_011520114.4	c.-53+190T>G		intron_variant
ART1	XM_017017763.3	c.-74+190T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ART1	ENST00000250693.2	c.-52-3317T>G		intron_variant		1	NM_004314.3	P1
ART1	ENST00000529556.1	n.204+190T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16061 AN: 151814 Hom.: 934 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.106 AC: 16066 AN: 151924 Hom.: 934 Cov.: 31 AF XY: 0.104 AC XY: 7696 AN XY: 74218

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.112

Alfa AF: 0.108 Hom.: 1373

Bravo AF: 0.108

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.8
Dann	Benign	0.82

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: rs16925377; hg19: chr11-3677075;