chr4-25260610-TTATATATATATATATA-T

Variant names:

• chr4-25260610-TTATATATATATATATA-T
• rs533544057
• NM_018323.4:c.978+36_978+51delTATATATATATATATA

Variant summary

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

The NM_018323.4(PI4K2B):​c.978+36_978+51delTATATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0079 in 306,796 control chromosomes in the GnomAD database, including 63 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.014 (44 hom., cov: 12)
  • Exomes 𝑓: 0.0031 (19 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4	c.978+36_978+51delTATATATATATATATA		intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2
PI4K2B	XM_005248174.3	c.963+36_963+51delTATATATATATATATA		intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5	c.690+36_690+51delTATATATATATATATA		intron_variant	Intron 6 of 9		XP_005248232.1
PI4K2B	NR_144633.2	n.1124+36_1124+51delTATATATATATATATA		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+35delTATATATATATATATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6
PI4K2B	ENST00000512921.4	c.690+20_690+35delTATATATATATATATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1

Frequencies

GnomAD3 genomes AF: 0.0139 AC: 1883 AN: 135084 Hom.: 44 Cov.: 12

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00661

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000238

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0210

Gnomad NFE AF: 0.000327

Gnomad OTH AF: 0.0136

GnomAD3 exomes AF: 0.00718 AC: 265 AN: 36926 Hom.: 25 AF XY: 0.00667 AC XY: 130 AN XY: 19504

Gnomad AFR exome AF: 0.0745

Gnomad AMR exome AF: 0.00574

Gnomad ASJ exome AF: 0.0317

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000412

Gnomad FIN exome AF: 0.000102

Gnomad NFE exome AF: 0.00166

Gnomad OTH exome AF: 0.0131

GnomAD4 exome AF: 0.00312 AC: 535 AN: 171700 Hom.: 19 AF XY: 0.00300 AC XY: 286 AN XY: 95490

Gnomad4 AFR exome AF: 0.0595

Gnomad4 AMR exome AF: 0.00578

Gnomad4 ASJ exome AF: 0.0155

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000526

Gnomad4 FIN exome AF: 0.000163

Gnomad4 NFE exome AF: 0.000962

Gnomad4 OTH exome AF: 0.00683

GnomAD4 genome AF: 0.0140 AC: 1888 AN: 135096 Hom.: 44 Cov.: 12 AF XY: 0.0138 AC XY: 891 AN XY: 64602

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.00661

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000239

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000327

Gnomad4 OTH AF: 0.0135

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;