4-25260610-TTATATATATATATATATATATA-TTATATATATATATATATATATATATATA

Variant names:

• chr4-25260610-T-TTATATA
• rs533544057
• NM_018323.4:c.978+46_978+51dupTATATA

Variant summary

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

The NM_018323.4(PI4K2B):​c.978+46_978+51dupTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0031 (1 hom., cov: 12)
  • Exomes 𝑓: 0.000087 (0 hom.)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 0 publications found

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]

ACMG classification

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+46_978+51dupTATATA		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.1124+46_1124+51dupTATATA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4K2B	ENST00000264864.8	TSL:1 MANE Select	c.978+19_978+20insTATATA		intron	N/A	ENSP00000264864.6	Q8TCG2
	PI4K2B	ENST00000871538.1		c.978+19_978+20insTATATA		intron	N/A	ENSP00000541597.1
	PI4K2B	ENST00000963199.1		c.963+19_963+20insTATATA		intron	N/A	ENSP00000633258.1

Frequencies

GnomAD3 genomes AF: 0.00313 AC: 422 AN: 135024 Hom.: 1 Cov.: 12

Gnomad AFR AF: 0.00600

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00185

Gnomad ASJ AF: 0.00211

Gnomad EAS AF: 0.00373

Gnomad SAS AF: 0.00334

Gnomad FIN AF: 0.000303

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00204

Gnomad OTH AF: 0.00545

GnomAD4 exome AF: 0.0000874 AC: 15 AN: 171718 Hom.: 0 Cov.: 0 AF XY: 0.0000942 AC XY: 9 AN XY: 95496

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

African (AFR) AF: 0.000249 AC: 1 AN: 4012

American (AMR) AF: 0.00 AC: 0 AN: 7096

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5406

East Asian (EAS) AF: 0.000118 AC: 1 AN: 8498

South Asian (SAS) AF: 0.00 AC: 0 AN: 7598

European-Finnish (FIN) AF: 0.0000813 AC: 2 AN: 24588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 618

European-Non Finnish (NFE) AF: 0.0000953 AC: 10 AN: 104964

Other (OTH) AF: 0.000112 AC: 1 AN: 8938

⚠️ 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.

GnomAD4 genome AF: 0.00312 AC: 421 AN: 135038 Hom.: 1 Cov.: 12 AF XY: 0.00288 AC XY: 186 AN XY: 64584

African (AFR) AF: 0.00599 AC: 217 AN: 36216

American (AMR) AF: 0.00177 AC: 23 AN: 13006

Ashkenazi Jewish (ASJ) AF: 0.00211 AC: 7 AN: 3318

East Asian (EAS) AF: 0.00375 AC: 17 AN: 4538

South Asian (SAS) AF: 0.00336 AC: 14 AN: 4172

European-Finnish (FIN) AF: 0.000303 AC: 2 AN: 6598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 264

European-Non Finnish (NFE) AF: 0.00204 AC: 131 AN: 64212

Other (OTH) AF: 0.00541 AC: 10 AN: 1850

Alfa AF: 0.00 Hom.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs533544057; hg19: chr4-25262232;