rs2255663

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-43536810-C-A
• chr15-43536810-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394395.1(PPIP5K1):​c.3671-1334G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394395.1. 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
	PPIP5K1	NM_001394395.1	MANE Select	c.3671-1334G>T		intron	N/A	NP_001381324.1	A0A8J8ZH50
	PPIP5K1	NM_001393969.1		c.3575-1334G>T		intron	N/A	NP_001380898.1	A0A9L9PYJ9
	PPIP5K1	NM_001393970.1		c.3575-1334G>T		intron	N/A	NP_001380899.1	A0A9L9PYJ9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPIP5K1	ENST00000420765.6	TSL:5 MANE Select	c.3671-1334G>T		intron	N/A	ENSP00000400887.2	A0A8J8ZH50
	PPIP5K1	ENST00000396923.7	TSL:1	c.3500-1334G>T		intron	N/A	ENSP00000380129.2	Q6PFW1-1
	PPIP5K1	ENST00000334933.8	TSL:1	c.3425-1334G>T		intron	N/A	ENSP00000334779.4	Q6PFW1-3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 5396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.60
PhyloP100		0.60

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2255663;

hg19: chr15-43829008;