Genetic Variant PI4K2B:c.978+44_978+51delTATATATA (chr4-25260610-TTATATATA-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018323.4(PI4K2B):c.978+44_978+51delTATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000946 in 306,680 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00081 ( 1 hom., cov: 12)

Exomes 𝑓: 0.0010 ( 1 hom. )

Consequence

PI4K2B
NM_018323.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.68

Publications

0 publications found

Variant links:

Genes affected

PI4K2B (HGNC:18215): (phosphatidylinositol 4-kinase type 2 beta) This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]

PI4K2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018323.4. 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
	PI4K2B	NM_018323.4	MANE Select	c.978+44_978+51delTATATATA		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.1124+44_1124+51delTATATATA		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PI4K2B	ENST00000264864.8	TSL:1 MANE Select	c.978+20_978+27delTATATATA	intron	N/A	ENSP00000264864.6	Q8TCG2
PI4K2B	ENST00000871538.1		c.978+20_978+27delTATATATA	intron	N/A	ENSP00000541597.1
PI4K2B	ENST00000963199.1		c.963+20_963+27delTATATATA	intron	N/A	ENSP00000633258.1

Frequencies

GnomAD3 genomes

AF:

0.000814

AC:

110

AN:

135096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000856

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00115

Gnomad ASJ

AF:

0.000301

Gnomad EAS

AF:

0.000658

Gnomad SAS

AF:

0.00548

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000498

Gnomad OTH

AF:

0.00272

GnomAD4 exome

AF:

0.00105

AC:

180

AN:

171572

Hom.:

AF XY:

0.00106

AC XY:

101

AN XY:

95420

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00125

AC:

AN:

4016

American (AMR)

AF:

0.000986

AC:

AN:

7096

Ashkenazi Jewish (ASJ)

AF:

0.00130

AC:

AN:

5398

East Asian (EAS)

AF:

0.000824

AC:

AN:

8494

South Asian (SAS)

AF:

0.00158

AC:

AN:

7596

European-Finnish (FIN)

AF:

0.000285

AC:

AN:

24582

Middle Eastern (MID)

AF:

0.00163

AC:

AN:

614

European-Non Finnish (NFE)

AF:

0.00122

AC:

128

AN:

104848

Other (OTH)

AF:

0.000672

AC:

AN:

8928

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.315

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:

0.000814

AC:

110

AN:

135108

Hom.:

Cov.:

AF XY:

0.000836

AC XY:

AN XY:

64612

show subpopulations

African (AFR)

AF:

0.000855

AC:

AN:

36254

American (AMR)

AF:

0.00115

AC:

AN:

13010

Ashkenazi Jewish (ASJ)

AF:

0.000301

AC:

AN:

3318

East Asian (EAS)

AF:

0.000660

AC:

AN:

4544

South Asian (SAS)

AF:

0.00550

AC:

AN:

4180

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

264

European-Non Finnish (NFE)

AF:

0.000498

AC:

AN:

64226

Other (OTH)

AF:

0.00270

AC:

AN:

1850

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.7

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over