6-33742507-C-T

Variant names:

• chr6-33742507-C-T
• rs6942022
• NM_054111.5:c.-180+4251G>A

Variant summary

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

The NM_054111.5(IP6K3):​c.-180+4251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,098 control chromosomes in the GnomAD database, including 1,151 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 0.11 (1151 hom., cov: 32)
• Consequence: IP6K3 NM_054111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 11 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_054111.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IP6K3	NM_054111.5	MANE Select	c.-180+4251G>A		intron	N/A	NP_473452.2	Q5TAQ4
	IP6K3	NM_001142883.2		c.-308-3246G>A		intron	N/A	NP_001136355.1	Q96PC2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IP6K3	ENST00000293756.5	TSL:1 MANE Select	c.-180+4251G>A		intron	N/A	ENSP00000293756.4	Q96PC2
	IP6K3	ENST00000451316.6	TSL:2	c.-308-3246G>A		intron	N/A	ENSP00000398861.1	Q96PC2
	IP6K3	ENST00000885829.1		c.-178+4251G>A		intron	N/A	ENSP00000555888.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16398 AN: 151980 Hom.: 1148 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.108 AC: 16430 AN: 152098 Hom.: 1151 Cov.: 32 AF XY: 0.108 AC XY: 8068 AN XY: 74364

African (AFR) AF: 0.193 AC: 8010 AN: 41448

American (AMR) AF: 0.0871 AC: 1333 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3472

East Asian (EAS) AF: 0.0461 AC: 238 AN: 5168

South Asian (SAS) AF: 0.0734 AC: 353 AN: 4812

European-Finnish (FIN) AF: 0.0949 AC: 1004 AN: 10578

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4853 AN: 68006

Other (OTH) AF: 0.105 AC: 222 AN: 2108

Alfa AF: 0.0829 Hom.: 2160

Bravo AF: 0.112

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.45
PhyloP100		-0.87
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: rs6942022; hg19: chr6-33710284;