Variant 5-103153807-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001276277.3(PPIP5K2):c.1131-41T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,400,242 control chromosomes in the GnomAD database, including 58,656 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 5025 hom., cov: 32)

Exomes 𝑓: 0.29 ( 53631 hom. )

Consequence

PPIP5K2
NM_001276277.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.109

Variant links:

Genes affected

PPIP5K2 (HGNC:29035): (diphosphoinositol pentakisphosphate kinase 2) This gene encodes a member of the histidine acid phosphatase family of proteins. Despite containing a histidine acid phosphatase domain, the encoded protein functions as an inositol pyrophosphate kinase, and is thought to lack phosphatase activity. This kinase activity is the mechanism by which the encoded protein synthesizes high-energy inositol pyrophosphates, which act as signaling molecules that regulate cellular homeostasis and other processes. This gene may be associated with autism spectrum disorder in human patients. [provided by RefSeq, Sep 2016]

PPIP5K2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 5-103153807-T-G is Benign according to our data. Variant chr5-103153807-T-G is described in ClinVar as [Benign]. Clinvar id is 1283907.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPIP5K2	NM_001276277.3 linkuse as main transcript	c.1131-41T>G		intron_variant		ENST00000358359.8	NP_001263206.1	O43314-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIP5K2	ENST00000358359.8 linkuse as main transcript	c.1131-41T>G		intron_variant		1	NM_001276277.3	ENSP00000351126.3		O43314-1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35641

AN:

151660

Hom.:

5027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0884

Gnomad AMI

AF:

0.429

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.233

GnomAD3 exomes

AF:

0.265

AC:

56980

AN:

214978

Hom.:

8272

AF XY:

0.265

AC XY:

31081

AN XY:

117280

show subpopulations

Gnomad AFR exome

AF:

0.0879

Gnomad AMR exome

AF:

0.203

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.446

Gnomad SAS exome

AF:

0.143

Gnomad FIN exome

AF:

0.335

Gnomad NFE exome

AF:

0.297

Gnomad OTH exome

AF:

0.259

GnomAD4 exome

AF:

0.286

AC:

356672

AN:

1248462

Hom.:

53631

Cov.:

AF XY:

0.282

AC XY:

177546

AN XY:

629768

show subpopulations

Gnomad4 AFR exome

AF:

0.0804

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.453

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.329

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.268

GnomAD4 genome

AF:

0.235

AC:

35646

AN:

151780

Hom.:

5025

Cov.:

AF XY:

0.234

AC XY:

17362

AN XY:

74140

show subpopulations

Gnomad4 AFR

AF:

0.0883

Gnomad4 AMR

AF:

0.229

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.449

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.301

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.194

Hom.:

874

Bravo

AF:

0.223

Asia WGS

AF:

0.253

AC:

873

AN:

3460

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.0

DANN

Benign

0.47

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over