rs72624940
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000883.4(IMPDH1):c.191-40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,614,138 control chromosomes in the GnomAD database, including 62 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 0.0094 ( 25 hom., cov: 33)
Exomes 𝑓: 0.00094 ( 37 hom. )
Consequence
IMPDH1
NM_000883.4 intron
NM_000883.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.528
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=-0.63).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00941 (1433/152330) while in subpopulation AFR AF= 0.0327 (1361/41566). AF 95% confidence interval is 0.0313. There are 25 homozygotes in gnomad4. There are 699 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1431 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPDH1 | NM_000883.4 | c.191-40G>A | intron_variant | ENST00000338791.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPDH1 | ENST00000338791.11 | c.191-40G>A | intron_variant | 2 | NM_000883.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00940 AC: 1431AN: 152212Hom.: 25 Cov.: 33
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GnomAD3 exomes AF: 0.00240 AC: 603AN: 251470Hom.: 14 AF XY: 0.00179 AC XY: 243AN XY: 135922
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GnomAD4 exome AF: 0.000936 AC: 1368AN: 1461808Hom.: 37 Cov.: 32 AF XY: 0.000793 AC XY: 577AN XY: 727208
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GnomAD4 genome ? AF: 0.00941 AC: 1433AN: 152330Hom.: 25 Cov.: 33 AF XY: 0.00938 AC XY: 699AN XY: 74490
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at