Variant 13-19467353-TAAAAAAAA-TAAAAAAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001395978.1(TPTE2):c.393-11_393-10dupTT 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 0.000023 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00021 ( 0 hom. )

Consequence

TPTE2
NM_001395978.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

TPTE2 (HGNC:17299): (transmembrane phosphoinositide 3-phosphatase and tensin homolog 2) TPIP is a member of a large class of membrane-associated phosphatases with substrate specificity for the 3-position phosphate of inositol phospholipids.[supplied by OMIM, Jul 2002]

TPTE2 links:

TPTE2 (HGNC:):

TPTE2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPTE2	NM_001395978.1 linkuse as main transcript	c.393-11_393-10dupTT		intron_variant		ENST00000697147.1	NP_001382907.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPTE2	ENST00000697147.1 linkuse as main transcript	c.393-11_393-10dupTT		intron_variant			NM_001395978.1	ENSP00000513136.1		Q6XPS3-1

Frequencies

GnomAD3 genomes

AF:

0.0000228

AC:

AN:

131678

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000276

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000329

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000673

AC:

AN:

32670

Hom.:

AF XY:

0.000591

AC XY:

AN XY:

16922

show subpopulations

Gnomad AFR exome

AF:

0.00109

Gnomad AMR exome

AF:

0.00241

Gnomad ASJ exome

AF:

0.000789

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000670

Gnomad FIN exome

AF:

0.000622

Gnomad NFE exome

AF:

0.000555

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000215

AC:

228

AN:

1061548

Hom.:

Cov.:

AF XY:

0.000218

AC XY:

113

AN XY:

518520

show subpopulations

Gnomad4 AFR exome

AF:

0.000264

Gnomad4 AMR exome

AF:

0.000545

Gnomad4 ASJ exome

AF:

0.000376

Gnomad4 EAS exome

AF:

0.0000780

Gnomad4 SAS exome

AF:

0.000497

Gnomad4 FIN exome

AF:

0.000281

Gnomad4 NFE exome

AF:

0.000193

Gnomad4 OTH exome

AF:

0.000254

GnomAD4 genome

AF:

0.0000228

AC:

AN:

131678

Hom.:

Cov.:

AF XY:

0.0000477

AC XY:

AN XY:

62932

show subpopulations

Gnomad4 AFR

AF:

0.0000276

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000329

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over