rs9853352

Positions:

• chr3-49775825-A-G

Variant summary

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

The NM_153273.4(IP6K1):​c.-129+10529T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,088 control chromosomes in the GnomAD database, including 663 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 0.087 (663 hom., cov: 30)
• Consequence: IP6K1 NM_153273.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

Genes affected

IP6K1 (HGNC:18360): (inositol hexakisphosphate kinase 1) This gene encodes a member of the inositol phosphokinase family. The encoded protein may be 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. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2011]

PHF5AP3 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.0994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IP6K1	NM_153273.4	c.-129+10529T>C		intron_variant		ENST00000321599.9	NP_695005.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IP6K1	ENST00000321599.9	c.-129+10529T>C		intron_variant		1	NM_153273.4	ENSP00000323780.4

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13186 AN: 151970 Hom.: 663 Cov.: 30

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0867 AC: 13186 AN: 152088 Hom.: 663 Cov.: 30 AF XY: 0.0857 AC XY: 6366 AN XY: 74322

Gnomad4 AFR AF: 0.0706

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0258

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0978

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.0864 Hom.: 106

Bravo AF: 0.0845

Asia WGS AF: 0.0340 AC: 122 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	4.1
DANN	Benign	0.77

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: rs9853352; hg19: chr3-49813258;