rs72624915

Variant names:

• chr3-49026122-G-A
• rs72624915
• NM_000884.3:c.1006+202C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-49026122-G-A
• chr3-49026122-G-C
• chr3-49026122-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NM_000884.3(IMPDH2):​c.1006+202C>T variant causes a intron change. The variant allele was found at a frequency of 0.0116 in 681,816 control chromosomes in the GnomAD database, including 92 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 0.0087 (6 hom., cov: 33)
  • Exomes 𝑓: 0.012 (86 hom.)
• Consequence: IMPDH2 NM_000884.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.95

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]

ENSG00000290315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00873 (1330/152346) while in subpopulation SAS AF= 0.0228 (110/4828). AF 95% confidence interval is 0.0193. There are 6 homozygotes in gnomad4. There are 682 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1330 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMPDH2	NM_000884.3	c.1006+202C>T		intron_variant	Intron 9 of 13	ENST00000326739.9	NP_000875.2
IMPDH2	NM_001410759.1	c.1007-56C>T		intron_variant	Intron 9 of 14		NP_001397688.1
IMPDH2	NM_001410760.1	c.932-56C>T		intron_variant	Intron 8 of 13		NP_001397689.1
IMPDH2	NM_001410761.1	c.931+202C>T		intron_variant	Intron 8 of 12		NP_001397690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMPDH2	ENST00000326739.9	c.1006+202C>T		intron_variant	Intron 9 of 13	1	NM_000884.3	ENSP00000321584.4
ENSG00000290315	ENST00000703936.1	c.3046+202C>T		intron_variant	Intron 17 of 21			ENSP00000515567.1

Frequencies

GnomAD3 genomes AF: 0.00872 AC: 1328 AN: 152228 Hom.: 6 Cov.: 33

Gnomad AFR AF: 0.00203

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.00739

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0139

GnomAD4 exome AF: 0.0124 AC: 6581 AN: 529470 Hom.: 86 Cov.: 0 AF XY: 0.0136 AC XY: 3916 AN XY: 287094

Gnomad4 AFR exome AF: 0.00123

Gnomad4 AMR exome AF: 0.00702

Gnomad4 ASJ exome AF: 0.0196

Gnomad4 EAS exome AF: 0.0000327

Gnomad4 SAS exome AF: 0.0250

Gnomad4 FIN exome AF: 0.0127

Gnomad4 NFE exome AF: 0.0116

Gnomad4 OTH exome AF: 0.0121

GnomAD4 genome AF: 0.00873 AC: 1330 AN: 152346 Hom.: 6 Cov.: 33 AF XY: 0.00916 AC XY: 682 AN XY: 74492

Gnomad4 AFR AF: 0.00202

Gnomad4 AMR AF: 0.00738

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.00526 Hom.: 2

Bravo AF: 0.00783

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
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

Other links and lift over

dbSNP: rs72624915; hg19: chr3-49063555;