rs3088189
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_021071.4(ART4):c.624C>T(p.Leu208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,613,800 control chromosomes in the GnomAD database, including 116,040 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.34 ( 9314 hom., cov: 32)
Exomes 𝑓: 0.38 ( 106726 hom. )
Consequence
ART4
NM_021071.4 synonymous
NM_021071.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.267
Genes affected
ART4 (HGNC:726): (ADP-ribosyltransferase 4 (inactive) (Dombrock blood group)) This gene encodes a protein that contains a mono-ADP-ribosylation (ART) motif. It is a member of the ADP-ribosyltransferase gene family but enzymatic activity has not been demonstrated experimentally. Antigens of the Dombrock blood group system are located on the gene product, which is glycosylphosphatidylinosotol-anchored to the erythrocyte membrane. Allelic variants, some of which lead to adverse transfusion reactions, are known. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 12-14840674-G-A is Benign according to our data. Variant chr12-14840674-G-A is described in ClinVar as [Benign]. Clinvar id is 3059324.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.267 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ART4 | NM_021071.4 | c.624C>T | p.Leu208= | synonymous_variant | 2/3 | ENST00000228936.6 | |
ART4 | NM_001354646.2 | c.624C>T | p.Leu208= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ART4 | ENST00000228936.6 | c.624C>T | p.Leu208= | synonymous_variant | 2/3 | 1 | NM_021071.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.340 AC: 51590AN: 151922Hom.: 9299 Cov.: 32
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GnomAD3 exomes AF: 0.347 AC: 87145AN: 250944Hom.: 16004 AF XY: 0.356 AC XY: 48291AN XY: 135606
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GnomAD4 exome AF: 0.377 AC: 550984AN: 1461760Hom.: 106726 Cov.: 56 AF XY: 0.378 AC XY: 275199AN XY: 727168
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GnomAD4 genome ? AF: 0.339 AC: 51616AN: 152040Hom.: 9314 Cov.: 32 AF XY: 0.336 AC XY: 24972AN XY: 74320
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ART4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at