chr15-43536810-C-T

Variant names:

• chr15-43536810-C-T
• rs2255663
• NM_001394395.1:c.3671-1334G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394395.1(PPIP5K1):​c.3671-1334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,044 control chromosomes in the GnomAD database, including 19,452 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (19452 hom., cov: 31)
• Consequence: PPIP5K1 NM_001394395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 22 publications found

Genes affected

PPIP5K1 (HGNC:29023): (diphosphoinositol pentakisphosphate kinase 1) This gene encodes a dual functional inositol kinase. The encoded enzyme converts inositol hexakisphosphate to diphosphoinositol pentakisphosphate and diphosphoinositol pentakisphosphate to bis-diphosphoinositol tetrakisphosphate. This protein may be important for intracellular signaling pathways. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 15.[provided by RefSeq, Jun 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIP5K1	NM_001394395.1	c.3671-1334G>A		intron_variant	Intron 31 of 31	ENST00000420765.6	NP_001381324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIP5K1	ENST00000420765.6	c.3671-1334G>A		intron_variant	Intron 31 of 31	5	NM_001394395.1	ENSP00000400887.2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67929 AN: 151926 Hom.: 19409 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.421

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.447 AC: 68023 AN: 152044 Hom.: 19452 Cov.: 31 AF XY: 0.440 AC XY: 32715 AN XY: 74308

African (AFR) AF: 0.816 AC: 33833 AN: 41486

American (AMR) AF: 0.360 AC: 5498 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1399 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2238 AN: 5160

South Asian (SAS) AF: 0.413 AC: 1994 AN: 4828

European-Finnish (FIN) AF: 0.205 AC: 2170 AN: 10566

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19652 AN: 67962

Other (OTH) AF: 0.423 AC: 893 AN: 2110

Alfa AF: 0.314 Hom.: 5396

Bravo AF: 0.477

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.7
DANN	Benign	0.63
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2255663; hg19: chr15-43829008;