rs72624937
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_000883.4(IMPDH1):c.-36T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,329,552 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 0.00076 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000069 ( 1 hom. )
Consequence
IMPDH1
NM_000883.4 5_prime_UTR
NM_000883.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.988
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000763 (116/152026) while in subpopulation AFR AF= 0.00263 (109/41468). AF 95% confidence interval is 0.00223. There are 0 homozygotes in gnomad4. There are 59 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 116 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPDH1 | NM_000883.4 | c.-36T>C | 5_prime_UTR_variant | 1/17 | ENST00000338791.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPDH1 | ENST00000338791.11 | c.-36T>C | 5_prime_UTR_variant | 1/17 | 2 | NM_000883.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000764 AC: 116AN: 151920Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000245 AC: 1AN: 4088Hom.: 0 AF XY: 0.000362 AC XY: 1AN XY: 2762
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GnomAD4 exome AF: 0.0000688 AC: 81AN: 1177526Hom.: 1 Cov.: 30 AF XY: 0.0000616 AC XY: 35AN XY: 567746
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GnomAD4 genome ? AF: 0.000763 AC: 116AN: 152026Hom.: 0 Cov.: 33 AF XY: 0.000794 AC XY: 59AN XY: 74314
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at