rs9853352

Variant names:

• chr3-49775825-A-G
• rs9853352
• NM_153273.4:c.-129+10529T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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:23267): (PHF5A pseudogene 3)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IP6K1	NM_153273.4	c.-129+10529T>C		intron_variant	Intron 1 of 5	ENST00000321599.9	NP_695005.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IP6K1	ENST00000321599.9	c.-129+10529T>C		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.0706 AC: 2930 AN: 41486

American (AMR) AF: 0.0713 AC: 1088 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3472

East Asian (EAS) AF: 0.0258 AC: 133 AN: 5164

South Asian (SAS) AF: 0.0571 AC: 275 AN: 4820

European-Finnish (FIN) AF: 0.0978 AC: 1034 AN: 10572

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6896 AN: 68002

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0862 Hom.: 109

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
PhyloP100		0.39
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: rs9853352; hg19: chr3-49813258;