Variant rs72624918 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_000884.3(IMPDH2):c.1296-23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,614,054 control chromosomes in the GnomAD database, including 142 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 0.0089 ( 8 hom., cov: 33)

Exomes 𝑓: 0.012 ( 134 hom. )

Consequence

IMPDH2
NM_000884.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

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]

IMPDH2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BS2

High AC in GnomAd4 at 1351 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
IMPDH2	NM_000884.3 linkuse as main transcript	c.1296-23C>T	intron_variant	ENST00000326739.9
IMPDH2	NM_001410759.1 linkuse as main transcript	c.1368-23C>T	intron_variant
IMPDH2	NM_001410760.1 linkuse as main transcript	c.1293-23C>T	intron_variant
IMPDH2	NM_001410761.1 linkuse as main transcript	c.1221-23C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMPDH2	ENST00000326739.9 linkuse as main transcript	c.1296-23C>T		intron_variant		1	NM_000884.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00888

AC:

1352

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00256

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00799

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.00915

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0144

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00897

AC:

2254

AN:

251222

Hom.:

AF XY:

0.00911

AC XY:

1237

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.00277

Gnomad AMR exome

AF:

0.00567

Gnomad ASJ exome

AF:

0.00348

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00154

Gnomad FIN exome

AF:

0.00916

Gnomad NFE exome

AF:

0.0148

Gnomad OTH exome

AF:

0.00930

GnomAD4 exome

AF:

0.0124

AC:

18189

AN:

1461744

Hom.:

134

Cov.:

AF XY:

0.0123

AC XY:

8912

AN XY:

727168

show subpopulations

Gnomad4 AFR exome

AF:

0.00155

Gnomad4 AMR exome

AF:

0.00610

Gnomad4 ASJ exome

AF:

0.00306

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00167

Gnomad4 FIN exome

AF:

0.00990

Gnomad4 NFE exome

AF:

0.0148

Gnomad4 OTH exome

AF:

0.0101

GnomAD4 genome

AF:

0.00887

AC:

1351

AN:

152310

Hom.:

Cov.:

AF XY:

0.00806

AC XY:

600

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00255

Gnomad4 AMR

AF:

0.00798

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00915

Gnomad4 NFE

AF:

0.0144

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00842

Hom.:

Bravo

AF:

0.00872

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.010

DANN

Benign

0.49

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over