11-3664425-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004314.3(ART1):​c.*236A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 316812 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 167036

African (AFR) AF: 0.00 AC: 0 AN: 8700

American (AMR) AF: 0.00 AC: 0 AN: 12798

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9670

East Asian (EAS) AF: 0.00 AC: 0 AN: 20418

South Asian (SAS) AF: 0.00 AC: 0 AN: 33312

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20376

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1408

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 191614

Other (OTH) AF: 0.00 AC: 0 AN: 18516

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		0.081

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;