Genetic Variant PI4K2B:c.978+34_978+51delTATATATATATATATATA (chr4-25260610-TTATATATATATATATATA-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

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. 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

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 made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4 link	c.978+34_978+51delTATATATATATATATATA	intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2	Q8TCG2
PI4K2B	XM_005248174.3 link	c.963+34_963+51delTATATATATATATATATA	intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5 link	c.690+34_690+51delTATATATATATATATATA	intron_variant	Intron 6 of 9		XP_005248232.1	G5E9Z4
PI4K2B	NR_144633.2 link	n.1124+34_1124+51delTATATATATATATATATA	intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8 link	c.978+20_978+37delTATATATATATATATATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6		Q8TCG2
PI4K2B	ENST00000512921.4 link	c.690+20_690+37delTATATATATATATATATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1		G5E9Z4

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

Gnomad4 AFR exome

AF:

0.00149

Gnomad4 AMR exome

AF:

0.000282

Gnomad4 ASJ exome

AF:

0.000370

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000191

Gnomad4 OTH exome

AF:

0.000336

GnomAD4 genome

AF:

0.00000740

AC:

AN:

135096

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

64584

show subpopulations

Gnomad4 AFR

AF:

0.0000276

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over