rs72624968
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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.1694+33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,613,944 control chromosomes in the GnomAD database, including 170 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 0.0099 ( 15 hom., cov: 32)
Exomes 𝑓: 0.014 ( 155 hom. )
Consequence
IMPDH1
NM_000883.4 intron
NM_000883.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.100
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=-0.64).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00987 (1502/152236) while in subpopulation NFE AF= 0.0149 (1016/68012). AF 95% confidence interval is 0.0142. There are 15 homozygotes in gnomad4. There are 692 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1502 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IMPDH1 | NM_000883.4 | c.1694+33C>T | intron_variant | ENST00000338791.11 | NP_000874.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IMPDH1 | ENST00000338791.11 | c.1694+33C>T | intron_variant | 2 | NM_000883.4 | ENSP00000345096.6 |
Frequencies
GnomAD3 genomes AF: 0.00987 AC: 1502AN: 152118Hom.: 15 Cov.: 32
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GnomAD3 exomes AF: 0.0103 AC: 2590AN: 251294Hom.: 20 AF XY: 0.0102 AC XY: 1392AN XY: 135838
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GnomAD4 exome AF: 0.0137 AC: 19962AN: 1461708Hom.: 155 Cov.: 34 AF XY: 0.0133 AC XY: 9660AN XY: 727158
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GnomAD4 genome AF: 0.00987 AC: 1502AN: 152236Hom.: 15 Cov.: 32 AF XY: 0.00930 AC XY: 692AN XY: 74418
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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