3-49026122-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000884.3(IMPDH2):​c.1006+202C>G variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

IMPDH2
NM_000884.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.95
Variant links:
Genes affected
IMPDH2 (HGNC:6053): (inosine monophosphate dehydrogenase 2) This gene encodes the rate-limiting enzyme in the de novo guanine nucleotide biosynthesis. It is thus involved in maintaining cellular guanine deoxy- and ribonucleotide pools needed for DNA and RNA synthesis. The encoded protein catalyzes the NAD-dependent oxidation of inosine-5'-monophosphate into xanthine-5'-monophosphate, which is then converted into guanosine-5'-monophosphate. This gene is up-regulated in some neoplasms, suggesting it may play a role in malignant transformation. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IMPDH2NM_000884.3 linkc.1006+202C>G intron_variant Intron 9 of 13 ENST00000326739.9 NP_000875.2 P12268A0A384N6C2
IMPDH2NM_001410759.1 linkc.1007-56C>G intron_variant Intron 9 of 14 NP_001397688.1
IMPDH2NM_001410760.1 linkc.932-56C>G intron_variant Intron 8 of 13 NP_001397689.1
IMPDH2NM_001410761.1 linkc.931+202C>G intron_variant Intron 8 of 12 NP_001397690.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IMPDH2ENST00000326739.9 linkc.1006+202C>G intron_variant Intron 9 of 13 1 NM_000884.3 ENSP00000321584.4 P12268
ENSG00000290315ENST00000703936.1 linkc.3046+202C>G intron_variant Intron 17 of 21 ENSP00000515567.1 A0A994J749

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
CADD
Uncertain
23
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72624915; hg19: chr3-49063555; API