rs16925377

Variant names:

• chr11-3655845-T-G
• rs16925377
• NM_004314.3:c.-52-3317T>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.-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
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004314.3. 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
	ART1	NM_004314.3	MANE Select	c.-52-3317T>G		intron	N/A	NP_004305.2	P52961

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ART1	ENST00000250693.2	TSL:1 MANE Select	c.-52-3317T>G		intron	N/A	ENSP00000250693.1	P52961
	ART1	ENST00000948756.1		c.-74+190T>G		intron	N/A	ENSP00000618815.1
	ART1	ENST00000948757.1		c.-73-3296T>G		intron	N/A	ENSP00000618816.1

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

African (AFR) AF: 0.128 AC: 5316 AN: 41426

American (AMR) AF: 0.0957 AC: 1460 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0341 AC: 164 AN: 4814

European-Finnish (FIN) AF: 0.0932 AC: 979 AN: 10508

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7358 AN: 67948

Other (OTH) AF: 0.112 AC: 236 AN: 2106

Alfa AF: 0.108 Hom.: 1841

Bravo AF: 0.108

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.82
PhyloP100		0.93
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: rs16925377; hg19: chr11-3677075;