dbSNP rs533544057: PI4K2B:c.978+30_978+51delTATATATATATATATATATATA (chr4-25260610-TTATATATATATATATATATATA-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+30_978+51delTATATATATATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000582 in 171,772 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: not found (cov: 12)

Exomes 𝑓: 0.0000058 ( 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+30_978+51delTATATATATATATATATATATA		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.1124+30_1124+51delTATATATATATATATATATATA		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+41delTATATATATATATATATATATA	intron	N/A	ENSP00000264864.6	Q8TCG2
PI4K2B	ENST00000871538.1		c.978+20_978+41delTATATATATATATATATATATA	intron	N/A	ENSP00000541597.1
PI4K2B	ENST00000963199.1		c.963+20_963+41delTATATATATATATATATATATA	intron	N/A	ENSP00000633258.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000582

AC:

AN:

171772

Hom.:

AF XY:

0.00

AC XY:

AN XY:

95528

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

4018

American (AMR)

AF:

0.00

AC:

AN:

7098

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5406

East Asian (EAS)

AF:

0.000118

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:

0.00

AC:

AN:

105000

Other (OTH)

AF:

0.00

AC:

AN:

8940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.7

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over