rs4672768
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004044.7(ATIC):c.1660-135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,570,326 control chromosomes in the GnomAD database, including 83,737 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 0.26 ( 5998 hom., cov: 32)
Exomes 𝑓: 0.33 ( 77739 hom. )
Consequence
ATIC
NM_004044.7 intron
NM_004044.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.415
Genes affected
ATIC (HGNC:794): (5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase) This gene encodes a bifunctional protein that catalyzes the last two steps of the de novo purine biosynthetic pathway. The N-terminal domain has phosphoribosylaminoimidazolecarboxamide formyltransferase activity, and the C-terminal domain has IMP cyclohydrolase activity. A mutation in this gene results in AICA-ribosiduria. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATIC | NM_004044.7 | c.1660-135G>A | intron_variant | ENST00000236959.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATIC | ENST00000236959.14 | c.1660-135G>A | intron_variant | 1 | NM_004044.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.257 AC: 39138AN: 152044Hom.: 5989 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.326 AC: 461873AN: 1418164Hom.: 77739 Cov.: 27 AF XY: 0.331 AC XY: 233876AN XY: 705636
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GnomAD4 genome ? AF: 0.257 AC: 39169AN: 152162Hom.: 5998 Cov.: 32 AF XY: 0.258 AC XY: 19179AN XY: 74388
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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