rs13005416
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004044.7(ATIC):c.689-1060G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 150,510 control chromosomes in the GnomAD database, including 18,903 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 0.48 ( 18903 hom., cov: 29)
Consequence
ATIC
NM_004044.7 intron
NM_004044.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.376
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATIC | NM_004044.7 | c.689-1060G>T | intron_variant | ENST00000236959.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATIC | ENST00000236959.14 | c.689-1060G>T | intron_variant | 1 | NM_004044.7 | P1 | |||
ATIC | ENST00000435675.5 | c.686-1060G>T | intron_variant | 2 | |||||
ATIC | ENST00000427397.5 | c.*582-1060G>T | intron_variant, NMD_transcript_variant | 5 | |||||
ATIC | ENST00000443953.5 | c.*786-1060G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.484 AC: 72740AN: 150412Hom.: 18873 Cov.: 29
GnomAD3 genomes
?
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72740
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150412
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.484 AC: 72813AN: 150510Hom.: 18903 Cov.: 29 AF XY: 0.487 AC XY: 35706AN XY: 73322
GnomAD4 genome
?
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72813
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150510
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29
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35706
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73322
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2436
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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