rs6457740

Variant names:

• chr6-33729348-A-G
• rs6457740
• NM_054111.5:c.200-1048T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-33729348-A-G
• chr6-33729348-A-T

Variant summary

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

The NM_054111.5(IP6K3):​c.200-1048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,134 control chromosomes in the GnomAD database, including 36,128 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 0.67 (36128 hom., cov: 32)
• Consequence: IP6K3 NM_054111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 17 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 (EAS) allele frequency at 95% confidence interval = 0.937 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.200-1048T>C		intron	N/A	NP_473452.2	Q5TAQ4
	IP6K3	NM_001142883.2		c.200-1048T>C		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.200-1048T>C		intron	N/A	ENSP00000293756.4	Q96PC2
	IP6K3	ENST00000451316.6	TSL:2	c.200-1048T>C		intron	N/A	ENSP00000398861.1	Q96PC2
	IP6K3	ENST00000885829.1		c.200-1048T>C		intron	N/A	ENSP00000555888.1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102289 AN: 152016 Hom.: 36118 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.673 AC: 102340 AN: 152134 Hom.: 36128 Cov.: 32 AF XY: 0.687 AC XY: 51058 AN XY: 74370

African (AFR) AF: 0.450 AC: 18648 AN: 41472

American (AMR) AF: 0.775 AC: 11854 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2652 AN: 3468

East Asian (EAS) AF: 0.960 AC: 4963 AN: 5172

South Asian (SAS) AF: 0.863 AC: 4167 AN: 4830

European-Finnish (FIN) AF: 0.834 AC: 8847 AN: 10610

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48932 AN: 67974

Other (OTH) AF: 0.690 AC: 1457 AN: 2112

Alfa AF: 0.718 Hom.: 84781

Bravo AF: 0.657

Asia WGS AF: 0.864 AC: 3006 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	2.4
DANN	Benign	0.75
PhyloP100		-0.053
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: rs6457740; hg19: chr6-33697125;