dbSNP rs2290692: ITPKC:c.*913G>A (chr19-40740473-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_025194.3(ITPKC):c.*913G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00478 in 204,292 control chromosomes in the GnomAD database, including 4 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 0.0047 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0051 ( 1 hom. )

Consequence

ITPKC
NM_025194.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95

Publications

22 publications found

Variant links:

Genes affected

ITPKC (HGNC:14897): (inositol-trisphosphate 3-kinase C) This gene encodes a member of the inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)] 3-kinase family of enzymes that catalyze the phosphorylation of inositol 1,4,5-trisphosphate to 1,3,4,5-tetrakisphosphate. The encoded protein is localized to the nucleus and cytoplasm and has both nuclear import and nuclear export activity. Single nucleotide polymorphisms in this gene are associated with Kawasaki disease.[provided by RefSeq, Sep 2009]

ITPKC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ITPKC	NM_025194.3 link	c.*913G>A	3_prime_UTR_variant	Exon 7 of 7	ENST00000263370.3	NP_079470.1	Q96DU7A0A024R0N8
ITPKC	NM_001411098.1 link	c.*913G>A	3_prime_UTR_variant	Exon 6 of 6		NP_001398027.1
ITPKC	XM_047439466.1 link	c.*543G>A	3_prime_UTR_variant	Exon 8 of 8		XP_047295422.1
ITPKC	XM_047439468.1 link	c.*1622G>A	3_prime_UTR_variant	Exon 7 of 7		XP_047295424.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPKC	ENST00000263370.3 link	c.*913G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_025194.3	ENSP00000263370.1		Q96DU7

Frequencies

GnomAD3 genomes

AF:

0.00468

AC:

711

AN:

152044

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000628

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00668

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00621

Gnomad FIN

AF:

0.00643

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00681

Gnomad OTH

AF:

0.00526

GnomAD4 exome

AF:

0.00512

AC:

267

AN:

52130

Hom.:

Cov.:

AF XY:

0.00451

AC XY:

122

AN XY:

27062

show subpopulations

African (AFR)

AF:

0.000669

AC:

AN:

1494

American (AMR)

AF:

0.00

AC:

AN:

1218

Ashkenazi Jewish (ASJ)

AF:

0.00112

AC:

AN:

1792

East Asian (EAS)

AF:

0.000220

AC:

AN:

4552

South Asian (SAS)

AF:

0.00426

AC:

AN:

470

European-Finnish (FIN)

AF:

0.00552

AC:

AN:

5976

Middle Eastern (MID)

AF:

0.00435

AC:

AN:

230

European-Non Finnish (NFE)

AF:

0.00655

AC:

218

AN:

33286

Other (OTH)

AF:

0.00289

AC:

AN:

3112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00467

AC:

710

AN:

152162

Hom.:

Cov.:

AF XY:

0.00485

AC XY:

361

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.000626

AC:

AN:

41534

American (AMR)

AF:

0.00667

AC:

102

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00230

AC:

AN:

3472

East Asian (EAS)

AF:

0.000194

AC:

AN:

5160

South Asian (SAS)

AF:

0.00601

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00643

AC:

AN:

10582

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00681

AC:

463

AN:

67988

Other (OTH)

AF:

0.00521

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

108

144

180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00821

Hom.:

960

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.034

(source)

DANN

Benign

0.40

PhyloP100

-2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over