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. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• 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

African (AFR) AF: 0.00123 AC: 19 AN: 15432

American (AMR) AF: 0.00702 AC: 238 AN: 33908

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 379 AN: 19376

East Asian (EAS) AF: 0.0000327 AC: 1 AN: 30592

South Asian (SAS) AF: 0.0250 AC: 1544 AN: 61726

European-Finnish (FIN) AF: 0.0127 AC: 405 AN: 31930

Middle Eastern (MID) AF: 0.0302 AC: 120 AN: 3974

European-Non Finnish (NFE) AF: 0.0116 AC: 3521 AN: 303184

Other (OTH) AF: 0.0121 AC: 354 AN: 29348

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

African (AFR) AF: 0.00202 AC: 84 AN: 41584

American (AMR) AF: 0.00738 AC: 113 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4828

European-Finnish (FIN) AF: 0.0160 AC: 170 AN: 10620

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 737 AN: 68038

Other (OTH) AF: 0.0137 AC: 29 AN: 2112

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
PhyloP100		6.0
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs72624915; hg19: chr3-49063555;