4-25260610-TTATATATATATATATATATA-TTATATATATATATATATATATA

Variant names:

• chr4-25260610-T-TTA
• rs533544057
• NM_018323.4:c.978+50_978+51dupTA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018323.4(PI4K2B):​c.978+50_978+51dupTA 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 0.065 (284 hom., cov: 12)
  • Exomes 𝑓: 0.0035 (0 hom.)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4	c.978+50_978+51dupTA		intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2
PI4K2B	XM_005248174.3	c.963+50_963+51dupTA		intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5	c.690+50_690+51dupTA		intron_variant	Intron 6 of 9		XP_005248232.1
PI4K2B	NR_144633.2	n.1124+50_1124+51dupTA		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8	c.978+19_978+20insTA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6
PI4K2B	ENST00000512921.4	c.690+19_690+20insTA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1

Frequencies

GnomAD3 genomes AF: 0.0650 AC: 8744 AN: 134448 Hom.: 283 Cov.: 12

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.0232

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0623

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.0780

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0544

GnomAD4 exome AF: 0.00354 AC: 606 AN: 171116 Hom.: 0 Cov.: 0 AF XY: 0.00366 AC XY: 348 AN XY: 95168

Gnomad4 AFR exome AF: 0.00350

Gnomad4 AMR exome AF: 0.00297

Gnomad4 ASJ exome AF: 0.00408

Gnomad4 EAS exome AF: 0.00520

Gnomad4 SAS exome AF: 0.00119

Gnomad4 FIN exome AF: 0.00389

Gnomad4 NFE exome AF: 0.00359

Gnomad4 OTH exome AF: 0.00269

GnomAD4 genome AF: 0.0650 AC: 8741 AN: 134460 Hom.: 284 Cov.: 12 AF XY: 0.0624 AC XY: 4016 AN XY: 64316

Gnomad4 AFR AF: 0.0635

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0619

Gnomad4 SAS AF: 0.0600

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.0540

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;