rs72624963
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000883.4(IMPDH1):c.1166-45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000524 in 1,468,756 control chromosomes in the GnomAD database, including 1 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 0.000059 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000052 ( 0 hom. )
Consequence
IMPDH1
NM_000883.4 intron
NM_000883.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
IMPDH1 (HGNC:6052): (inosine monophosphate dehydrogenase 1) The protein encoded by this gene acts as a homotetramer to regulate cell growth. The encoded protein is an enzyme that catalyzes the synthesis of xanthine monophosphate (XMP) from inosine-5'-monophosphate (IMP). This is the rate-limiting step in the de novo synthesis of guanine nucleotides. Defects in this gene are a cause of retinitis pigmentosa type 10 (RP10). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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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=-0.81).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000591 (9/152180) while in subpopulation EAS AF= 0.00135 (7/5204). AF 95% confidence interval is 0.000631. There are 1 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPDH1 | NM_000883.4 | c.1166-45G>A | intron_variant | ENST00000338791.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPDH1 | ENST00000338791.11 | c.1166-45G>A | intron_variant | 2 | NM_000883.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152180Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000242 AC: 37AN: 153044Hom.: 1 AF XY: 0.000284 AC XY: 23AN XY: 80964
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GnomAD4 exome AF: 0.0000516 AC: 68AN: 1316576Hom.: 0 Cov.: 22 AF XY: 0.0000644 AC XY: 42AN XY: 652134
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GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152180Hom.: 1 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at