Genetic Variant NM_004314.3:c.*236A>T (chr11-3664425-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0810

Publications

6 publications found

Variant links:

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]

ART1 links:

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ACMG classification

Classification was made for transcript

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	Effect	MANE	Protein	UniProt
ART1	NM_004314.3 link	c.*236A>T	downstream_gene_variant	ENST00000250693.2	NP_004305.2	P52961
ART1	XM_011520114.4 link	c.*236A>T	downstream_gene_variant		XP_011518416.1	P52961
ART1	XM_017017763.3 link	c.*236A>T	downstream_gene_variant		XP_016873252.1	P52961

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART1	ENST00000250693.2 link	c.*236A>T		downstream_gene_variant		1	NM_004314.3	ENSP00000250693.1		P52961

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

316812

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

167036

African (AFR)

AF:

0.00

AC:

AN:

8700

American (AMR)

AF:

0.00

AC:

AN:

12798

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9670

East Asian (EAS)

AF:

0.00

AC:

AN:

20418

South Asian (SAS)

AF:

0.00

AC:

AN:

33312

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20376

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1408

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

191614

Other (OTH)

AF:

0.00

AC:

AN:

18516

GnomAD4 genome

Cov.:

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

(source)

DANN

Benign

0.54

PhyloP100

0.081

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over