14-93099471-A-G

Variant names:

• chr14-93099471-A-G
• rs957362
• NM_014216.6:c.95+15598T>C

Variant summary

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

The NM_014216.6(ITPK1):​c.95+15598T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,044 control chromosomes in the GnomAD database, including 7,431 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 0.29 (7431 hom., cov: 32)
• Consequence: ITPK1 NM_014216.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 7 publications found

Genes affected

ITPK1 (HGNC:6177): (inositol-tetrakisphosphate 1-kinase) This gene encodes an enzyme that belongs to the inositol 1,3,4-trisphosphate 5/6-kinase family. This enzyme regulates the synthesis of inositol tetraphosphate, and downstream products, inositol pentakisphosphate and inositol hexakisphosphate. Inositol metabolism plays a role in the development of the neural tube. Disruptions in this gene are thought to be associated with neural tube defects. A pseudogene of this gene has been identified on chromosome X. [provided by RefSeq, Jul 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014216.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITPK1	NM_014216.6	MANE Select	c.95+15598T>C		intron	N/A	NP_055031.2
	ITPK1	NM_001142593.3		c.95+15598T>C		intron	N/A	NP_001136065.1
	ITPK1	NM_001142594.3		c.95+15598T>C		intron	N/A	NP_001136066.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITPK1	ENST00000267615.11	TSL:1 MANE Select	c.95+15598T>C		intron	N/A	ENSP00000267615.5
	ITPK1	ENST00000556603.6	TSL:1	c.95+15598T>C		intron	N/A	ENSP00000451091.1
	ITPK1	ENST00000354313.7	TSL:1	c.95+15598T>C		intron	N/A	ENSP00000346272.3

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44594 AN: 151926 Hom.: 7408 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.294 AC: 44670 AN: 152044 Hom.: 7431 Cov.: 32 AF XY: 0.294 AC XY: 21832 AN XY: 74352

African (AFR) AF: 0.462 AC: 19129 AN: 41448

American (AMR) AF: 0.274 AC: 4179 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3470

East Asian (EAS) AF: 0.149 AC: 769 AN: 5160

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2296 AN: 10580

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14824 AN: 67976

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.240 Hom.: 19872

Bravo AF: 0.305

Asia WGS AF: 0.283 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		0.028
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: rs957362; hg19: chr14-93565816;