rs9969804

Variant names:

• chr9-92666838-A-C
• rs9969804
• NM_022755.6:c.81+3070T>G

Variant summary

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

The NM_022755.6(IPPK):​c.81+3070T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,774 control chromosomes in the GnomAD database, including 36,298 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 0.68 (36298 hom., cov: 31)
• Consequence: IPPK NM_022755.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 51 publications found

Genes affected

IPPK (HGNC:14645): (inositol-pentakisphosphate 2-kinase) The protein encoded by this gene is a kinase that phosphorylates position 2 of inositol-1,3,4,5,6-pentakisphosphate to form inositol-1,2,3,4,5,6-hexakisphosphate (InsP6). InsP6 has a variety of functions, including stimulation of DNA repair, endocytosis, and mRNA export. [provided by RefSeq, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPPK	NM_022755.6	c.81+3070T>G		intron_variant	Intron 1 of 12	ENST00000287996.8	NP_073592.1
IPPK	XM_017015041.2	c.81+3070T>G		intron_variant	Intron 1 of 13		XP_016870530.1
IPPK	XM_047423732.1	c.81+3070T>G		intron_variant	Intron 1 of 9		XP_047279688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPPK	ENST00000287996.8	c.81+3070T>G		intron_variant	Intron 1 of 12	1	NM_022755.6	ENSP00000287996.3
IPPK	ENST00000375522.2	n.81+3070T>G		intron_variant	Intron 1 of 12	3		ENSP00000364672.2

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102351 AN: 151658 Hom.: 36244 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.675 AC: 102456 AN: 151774 Hom.: 36298 Cov.: 31 AF XY: 0.673 AC XY: 49902 AN XY: 74172

African (AFR) AF: 0.894 AC: 37055 AN: 41446

American (AMR) AF: 0.626 AC: 9552 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2362 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4490 AN: 5146

South Asian (SAS) AF: 0.653 AC: 3142 AN: 4808

European-Finnish (FIN) AF: 0.511 AC: 5364 AN: 10488

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38170 AN: 67852

Other (OTH) AF: 0.670 AC: 1408 AN: 2102

Alfa AF: 0.610 Hom.: 127557

Bravo AF: 0.697

Asia WGS AF: 0.771 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.67
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: rs9969804; hg19: chr9-95429120;