Genetic Variant PI4K2B:c.978+34_978+51delTATATATATATATATATA (chr4-25260610-TTATATATATATATATATA-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+34_978+51delTATATATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 306,850 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000074 ( 0 hom., cov: 12)

Exomes 𝑓: 0.000087 ( 0 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+34_978+51delTATATATATATATATATA		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.1124+34_1124+51delTATATATATATATATATA		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+37delTATATATATATATATATA	intron	N/A	ENSP00000264864.6	Q8TCG2
PI4K2B	ENST00000871538.1		c.978+20_978+37delTATATATATATATATATA	intron	N/A	ENSP00000541597.1
PI4K2B	ENST00000963199.1		c.963+20_963+37delTATATATATATATATATA	intron	N/A	ENSP00000633258.1

Frequencies

GnomAD3 genomes

AF:

0.00000740

AC:

AN:

135096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000276

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000873

AC:

AN:

171754

Hom.:

AF XY:

0.0000942

AC XY:

AN XY:

95520

show subpopulations

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

African (AFR)

AF:

0.00149

AC:

AN:

4018

American (AMR)

AF:

0.000282

AC:

AN:

7096

Ashkenazi Jewish (ASJ)

AF:

0.000370

AC:

AN:

5404

East Asian (EAS)

AF:

0.00

AC:

AN:

8498

South Asian (SAS)

AF:

0.00

AC:

AN:

7598

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24596

Middle Eastern (MID)

AF:

0.00

AC:

AN:

618

European-Non Finnish (NFE)

AF:

0.0000191

AC:

AN:

104986

Other (OTH)

AF:

0.000336

AC:

AN:

8940

⚠️ 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: 0.285

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:

0.00000740

AC:

AN:

135096

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

64584

show subpopulations

African (AFR)

AF:

0.0000276

AC:

AN:

36194

American (AMR)

AF:

0.00

AC:

AN:

13002

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3318

East Asian (EAS)

AF:

0.00

AC:

AN:

4562

South Asian (SAS)

AF:

0.00

AC:

AN:

4198

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64238

Other (OTH)

AF:

0.00

AC:

AN:

1836

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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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4-25260610-TTATATATATATATATATATATA-TTATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over