dbSNP rs533544057: PI4K2B:c.978+30_978+51delTATATATATATATATATATATA (chr4-25260610-TTATATATATATATATATATATA-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+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. 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

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+30_978+51delTATATATATATATATATATATA	intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2	Q8TCG2
PI4K2B	XM_005248174.3 link	c.963+30_963+51delTATATATATATATATATATATA	intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5 link	c.690+30_690+51delTATATATATATATATATATATA	intron_variant	Intron 6 of 9		XP_005248232.1	G5E9Z4
PI4K2B	NR_144633.2 link	n.1124+30_1124+51delTATATATATATATATATATATA	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+41delTATATATATATATATATATATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6		Q8TCG2
PI4K2B	ENST00000512921.4 link	c.690+20_690+41delTATATATATATATATATATATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1		G5E9Z4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000582

AC:

AN:

171772

Hom.:

AF XY:

0.00

AC XY:

AN XY:

95528

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000118

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over