rs9969804

Positions:

• chr9-92666838-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IPPK	NM_022755.6	c.81+3070T>G		intron_variant		ENST00000287996.8
IPPK	XM_017015041.2	c.81+3070T>G		intron_variant
IPPK	XM_047423732.1	c.81+3070T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPPK	ENST00000287996.8	c.81+3070T>G		intron_variant		1	NM_022755.6	P1
IPPK	ENST00000375522.2	c.81+3070T>G		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.670

Alfa AF: 0.598 Hom.: 60007

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

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: rs9969804; hg19: chr9-95429120;