4-76013587-G-C

Variant names:

• chr4-76013587-G-C
• rs867562
• ENST00000341029.9:c.-10+2267G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001130017.3(ART3):​c.-10+2267G>C variant causes a intron 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: 32)
• Consequence: ART3 NM_001130017.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

Genes affected

ART3 (HGNC:725): (ADP-ribosyltransferase 3 (inactive)) This gene encodes an arginine-specific ADP-ribosyltransferase. The encoded protein catalyzes a reversible reaction which modifies proteins by the addition or removal of ADP-ribose to an arginine residue to regulate the function of the modified protein. An ADP-ribosyltransferase pseudogene is located on chromosome 11. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ART3	NM_001130017.3	c.-10+2267G>C		intron_variant	Intron 1 of 9		NP_001123489.1
ART3	NM_001377177.1	c.-10+2267G>C		intron_variant	Intron 1 of 7		NP_001364106.1
ART3	NM_001377181.1	c.-10+2267G>C		intron_variant	Intron 1 of 5		NP_001364110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ART3	ENST00000341029.9	c.-10+2267G>C		intron_variant	Intron 1 of 9	1		ENSP00000343843.5
ART3	ENST00000513122.5	c.-125+2267G>C		intron_variant	Intron 1 of 4	1		ENSP00000422287.1
ART3	ENST00000513353.5	c.-44+2267G>C		intron_variant	Intron 1 of 3	1		ENSP00000421345.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867562; hg19: chr4-76934740;