Genetic Variant TPTE2:c.393-10dupT (chr13-19467352-AT-ATA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001395978.1(TPTE2):c.393-10dupT 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 0.0011 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0041 ( 0 hom. )

Consequence

TPTE2
NM_001395978.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

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]

TPTE2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395978.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TPTE2	NM_001395978.1	MANE Select	c.393-10dupT	intron	N/A	NP_001382907.1	Q6XPS3-1
TPTE2	NM_199254.3		c.393-10dupT	intron	N/A	NP_954863.2	Q6XPS3-1
TPTE2	NM_130785.4		c.282-1790dupT	intron	N/A	NP_570141.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TPTE2	ENST00000697147.1	MANE Select	c.393-10_393-9insT	intron	N/A	ENSP00000513136.1	Q6XPS3-1
TPTE2	ENST00000390680.2	TSL:1	c.282-1790_282-1789insT	intron	N/A	ENSP00000375098.2	Q6XPS3-3
TPTE2	ENST00000696858.2		c.393-10_393-9insT	intron	N/A	ENSP00000512931.1	Q6XPS3-1

Frequencies

GnomAD3 genomes

AF:

0.00105

AC:

138

AN:

131676

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00174

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00166

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000454

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000608

Gnomad OTH

AF:

0.00331

GnomAD2 exomes

AF:

0.00618

AC:

202

AN:

32670

AF XY:

0.00597

show subpopulations

Gnomad AFR exome

AF:

0.0136

Gnomad AMR exome

AF:

0.00663

Gnomad ASJ exome

AF:

0.000789

Gnomad EAS exome

AF:

0.00600

Gnomad FIN exome

AF:

0.00647

Gnomad NFE exome

AF:

0.00555

Gnomad OTH exome

AF:

0.0145

GnomAD4 exome

AF:

0.00405

AC:

4284

AN:

1057200

Hom.:

Cov.:

AF XY:

0.00412

AC XY:

2126

AN XY:

516382

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00947

AC:

214

AN:

22598

American (AMR)

AF:

0.00528

AC:

AN:

10982

Ashkenazi Jewish (ASJ)

AF:

0.00465

AC:

AN:

15906

East Asian (EAS)

AF:

0.00282

AC:

AN:

25560

South Asian (SAS)

AF:

0.00414

AC:

166

AN:

40118

European-Finnish (FIN)

AF:

0.00649

AC:

230

AN:

35418

Middle Eastern (MID)

AF:

0.00764

AC:

AN:

3666

European-Non Finnish (NFE)

AF:

0.00375

AC:

3224

AN:

859754

Other (OTH)

AF:

0.00505

AC:

218

AN:

43198

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.282

Heterozygous variant carriers

368

736

1104

1472

1840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

106

212

318

424

530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00106

AC:

140

AN:

131678

Hom.:

Cov.:

AF XY:

0.00116

AC XY:

AN XY:

62962

show subpopulations

African (AFR)

AF:

0.00179

AC:

AN:

36358

American (AMR)

AF:

0.00165

AC:

AN:

13296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3196

East Asian (EAS)

AF:

0.00155

AC:

AN:

4528

South Asian (SAS)

AF:

0.00

AC:

AN:

3998

European-Finnish (FIN)

AF:

0.000454

AC:

AN:

6608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

248

European-Non Finnish (NFE)

AF:

0.000608

AC:

AN:

60808

Other (OTH)

AF:

0.00330

AC:

AN:

1820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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.

Publications

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chr13-19467353-T-TAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over