10-58265894-T-C

Variant names:

• chr10-58265894-T-C
• rs2790169
• NM_152230.5:c.190+1528A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152230.5(IPMK):​c.190+1528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,074 control chromosomes in the GnomAD database, including 10,962 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 0.34 (10962 hom., cov: 32)
• Consequence: IPMK NM_152230.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 10 publications found

Genes affected

IPMK (HGNC:20739): (inositol polyphosphate multikinase) This gene encodes a member of the inositol phosphokinase family. The encoded protein has 3-kinase, 5-kinase and 6-kinase activities on phosphorylated inositol substrates. The encoded protein plays an important role in the biosynthesis of inositol 1,3,4,5,6-pentakisphosphate, and has a preferred 5-kinase activity. This gene may play a role in nuclear mRNA export. Pseudogenes of this gene are located on the long arm of chromosome 13 and the short arm of chromosome 19. [provided by RefSeq, Dec 2010]

IPMK Gene-Disease associations (from GenCC):

• hereditary neuroendocrine tumor of small intestine

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152230.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPMK	NM_152230.5	MANE Select	c.190+1528A>G		intron	N/A	NP_689416.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPMK	ENST00000373935.4	TSL:1 MANE Select	c.190+1528A>G		intron	N/A	ENSP00000363046.3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51385 AN: 151956 Hom.: 10928 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.286

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.338 AC: 51473 AN: 152074 Hom.: 10962 Cov.: 32 AF XY: 0.338 AC XY: 25110 AN XY: 74340

African (AFR) AF: 0.607 AC: 25184 AN: 41456

American (AMR) AF: 0.235 AC: 3595 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 786 AN: 3472

East Asian (EAS) AF: 0.446 AC: 2306 AN: 5174

South Asian (SAS) AF: 0.275 AC: 1327 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2323 AN: 10588

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15104 AN: 67978

Other (OTH) AF: 0.284 AC: 601 AN: 2114

Alfa AF: 0.315 Hom.: 1171

Bravo AF: 0.352

Asia WGS AF: 0.321 AC: 1118 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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: rs2790169; hg19: chr10-60025654;