Genetic Variant TPTE2:c.393-14_393-10delTTTTT (chr13-19467353-TAAAAA-T) – 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.393-14_393-10delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,192,980 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000061 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00017 ( 0 hom. )

Consequence

TPTE2
NM_001395978.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.69

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:

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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.393-14_393-10delTTTTT	intron	N/A	NP_001382907.1	Q6XPS3-1
TPTE2	NM_199254.3		c.393-14_393-10delTTTTT	intron	N/A	NP_954863.2	Q6XPS3-1
TPTE2	NM_130785.4		c.282-1794_282-1790delTTTTT	intron	N/A	NP_570141.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TPTE2	ENST00000697147.1	MANE Select	c.393-14_393-10delTTTTT	intron	N/A	ENSP00000513136.1	Q6XPS3-1
TPTE2	ENST00000390680.2	TSL:1	c.282-1794_282-1790delTTTTT	intron	N/A	ENSP00000375098.2	Q6XPS3-3
TPTE2	ENST00000696858.2		c.393-14_393-10delTTTTT	intron	N/A	ENSP00000512931.1	Q6XPS3-1

Frequencies

GnomAD3 genomes

AF:

0.0000608

AC:

AN:

131682

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000220

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000167

AC:

177

AN:

1061296

Hom.:

AF XY:

0.000191

AC XY:

AN XY:

518380

show subpopulations

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

African (AFR)

AF:

0.000793

AC:

AN:

22686

American (AMR)

AF:

0.000819

AC:

AN:

10990

Ashkenazi Jewish (ASJ)

AF:

0.000439

AC:

AN:

15952

East Asian (EAS)

AF:

0.000117

AC:

AN:

25602

South Asian (SAS)

AF:

0.000572

AC:

AN:

40220

European-Finnish (FIN)

AF:

0.000197

AC:

AN:

35544

Middle Eastern (MID)

AF:

0.000544

AC:

AN:

3676

European-Non Finnish (NFE)

AF:

0.000117

AC:

101

AN:

863294

Other (OTH)

AF:

0.000162

AC:

AN:

43332

⚠️ 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: 0.260

Heterozygous variant carriers

102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.0000608

AC:

AN:

131684

Hom.:

Cov.:

AF XY:

0.0000794

AC XY:

AN XY:

62968

show subpopulations

African (AFR)

AF:

0.000220

AC:

AN:

36358

American (AMR)

AF:

0.00

AC:

AN:

13296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3196

East Asian (EAS)

AF:

0.00

AC:

AN:

4530

South Asian (SAS)

AF:

0.00

AC:

AN:

3998

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

248

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

60812

Other (OTH)

AF:

0.00

AC:

AN:

1820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.544

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

1.7

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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13-19467353-TAAAAAAAA-TAAA

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