rs791903

chr6-33734868-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_054111.5(IP6K3):c.199+410C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,120 control chromosomes in the GnomAD database, including 22,131 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 0.52 (22131 hom., cov: 32)
• Consequence: IP6K3 NM_054111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970

Genes affected

IP6K3 (HGNC:17269): (inositol hexakisphosphate kinase 3) This gene encodes a protein that belongs to the inositol phosphokinase (IPK) family. This protein is likely responsible for the conversion of inositol hexakisphosphate (InsP6) to diphosphoinositol pentakisphosphate (InsP7/PP-InsP5). It may also convert 1,3,4,5,6-pentakisphosphate (InsP5) to PP-InsP4. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IP6K3	NM_054111.5	c.199+410C>G		intron_variant		ENST00000293756.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IP6K3	ENST00000293756.5	c.199+410C>G		intron_variant		1	NM_054111.5	P1
IP6K3	ENST00000451316.6	c.199+410C>G		intron_variant		2		P1
IP6K3	ENST00000634274.1	c.199+410C>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79589 AN: 152002 Hom.: 22099 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.524 AC: 79686 AN: 152120 Hom.: 22131 Cov.: 32 AF XY: 0.507 AC XY: 37711 AN XY: 74376

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.531

Alfa AF: 0.534 Hom.: 2775

Bravo AF: 0.536

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.58
Dann	Benign	0.63

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: rs791903; hg19: chr6-33702645;