rs71092363

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001395978.1(TPTE2):​c.393-17_393-10delTTTTTTTT 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: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TPTE2
NM_001395978.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.79

Publications

0 publications found
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TPTE2NM_001395978.1 linkc.393-17_393-10delTTTTTTTT intron_variant Intron 9 of 22 ENST00000697147.1 NP_001382907.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TPTE2ENST00000697147.1 linkc.393-17_393-10delTTTTTTTT intron_variant Intron 9 of 22 NM_001395978.1 ENSP00000513136.1 Q6XPS3-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1062184
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
518820
African (AFR)
AF:
0.00
AC:
0
AN:
22708
American (AMR)
AF:
0.00
AC:
0
AN:
11016
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15978
East Asian (EAS)
AF:
0.00
AC:
0
AN:
25646
South Asian (SAS)
AF:
0.00
AC:
0
AN:
40292
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35596
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3676
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
863900
Other (OTH)
AF:
0.00
AC:
0
AN:
43372
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493; API