rs7123164

Variant names:

• chr11-3657216-G-A
• rs7123164
• NM_004314.3:c.-52-1946G>A

Variant summary

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

The NM_004314.3(ART1):​c.-52-1946G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,114 control chromosomes in the GnomAD database, including 1,618 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 0.14 (1618 hom., cov: 32)
• Consequence: ART1 NM_004314.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART1	NM_004314.3	c.-52-1946G>A		intron_variant	Intron 1 of 4	ENST00000250693.2	NP_004305.2
ART1	XM_011520114.4	c.-53+1561G>A		intron_variant	Intron 2 of 5		XP_011518416.1
ART1	XM_017017763.3	c.-74+1561G>A		intron_variant	Intron 2 of 5		XP_016873252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART1	ENST00000250693.2	c.-52-1946G>A		intron_variant	Intron 1 of 4	1	NM_004314.3	ENSP00000250693.1
ART1	ENST00000529556.1	n.204+1561G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21202 AN: 151996 Hom.: 1616 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.139 AC: 21217 AN: 152114 Hom.: 1618 Cov.: 32 AF XY: 0.141 AC XY: 10499 AN XY: 74360

African (AFR) AF: 0.187 AC: 7771 AN: 41476

American (AMR) AF: 0.0865 AC: 1323 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3468

East Asian (EAS) AF: 0.168 AC: 868 AN: 5164

South Asian (SAS) AF: 0.193 AC: 928 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10584

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7778 AN: 67994

Other (OTH) AF: 0.130 AC: 275 AN: 2112

Alfa AF: 0.124 Hom.: 831

Bravo AF: 0.136

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		0.14
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: rs7123164; hg19: chr11-3678446;