chr4-25260610-TTATATATATATATA-T

Variant names:

• chr4-25260610-TTATATATATATATA-T
• rs533544057
• NM_018323.4:c.978+38_978+51delTATATATATATATA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_018323.4(PI4K2B):​c.978+38_978+51delTATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00572 in 306,722 control chromosomes in the GnomAD database, including 29 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0050 (4 hom., cov: 12)
  • Exomes 𝑓: 0.0063 (25 hom.)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4	c.978+38_978+51delTATATATATATATA		intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2
PI4K2B	XM_005248174.3	c.963+38_963+51delTATATATATATATA		intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5	c.690+38_690+51delTATATATATATATA		intron_variant	Intron 6 of 9		XP_005248232.1
PI4K2B	NR_144633.2	n.1124+38_1124+51delTATATATATATATA		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8	c.978+20_978+33delTATATATATATATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6
PI4K2B	ENST00000512921.4	c.690+20_690+33delTATATATATATATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1

Frequencies

GnomAD3 genomes AF: 0.00496 AC: 670 AN: 135092 Hom.: 4 Cov.: 12

Gnomad AFR AF: 0.00298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00177

Gnomad ASJ AF: 0.00814

Gnomad EAS AF: 0.000219

Gnomad SAS AF: 0.00453

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00648

Gnomad OTH AF: 0.00436

GnomAD3 exomes AF: 0.00723 AC: 267 AN: 36926 Hom.: 5 AF XY: 0.00769 AC XY: 150 AN XY: 19504

Gnomad AFR exome AF: 0.00443

Gnomad AMR exome AF: 0.00328

Gnomad ASJ exome AF: 0.00951

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00577

Gnomad FIN exome AF: 0.0114

Gnomad NFE exome AF: 0.00663

Gnomad OTH exome AF: 0.00933

GnomAD4 exome AF: 0.00630 AC: 1082 AN: 171618 Hom.: 25 AF XY: 0.00636 AC XY: 607 AN XY: 95428

Gnomad4 AFR exome AF: 0.00499

Gnomad4 AMR exome AF: 0.00225

Gnomad4 ASJ exome AF: 0.00703

Gnomad4 EAS exome AF: 0.000118

Gnomad4 SAS exome AF: 0.00818

Gnomad4 FIN exome AF: 0.00818

Gnomad4 NFE exome AF: 0.00642

Gnomad4 OTH exome AF: 0.00717

GnomAD4 genome AF: 0.00497 AC: 671 AN: 135104 Hom.: 4 Cov.: 12 AF XY: 0.00515 AC XY: 333 AN XY: 64608

Gnomad4 AFR AF: 0.00301

Gnomad4 AMR AF: 0.00177

Gnomad4 ASJ AF: 0.00814

Gnomad4 EAS AF: 0.000220

Gnomad4 SAS AF: 0.00455

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.00648

Gnomad4 OTH AF: 0.00432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs533544057; hg19: chr4-25262232;