13-19467353-TAAAAAAAA-TAAAA

Variant names:

• chr13-19467353-TAAAA-T
• rs71092363
• NM_001395978.1:c.393-13_393-10delTTTT

Variant summary

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

The NM_001395978.1(TPTE2):​c.393-13_393-10delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,187,684 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 0.00026 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0018 (0 hom.)
• Consequence: TPTE2 NM_001395978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 0 publications found

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]

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPTE2	NM_001395978.1	c.393-13_393-10delTTTT		intron_variant	Intron 9 of 22	ENST00000697147.1	NP_001382907.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPTE2	ENST00000697147.1	c.393-13_393-10delTTTT		intron_variant	Intron 9 of 22		NM_001395978.1	ENSP00000513136.1

Frequencies

GnomAD3 genomes AF: 0.000251 AC: 33 AN: 131682 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000744

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000753

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000493

Gnomad OTH AF: 0.000552

GnomAD2 exomes AF: 0.00490 AC: 160 AN: 32670 AF XY: 0.00485

Gnomad AFR exome AF: 0.0174

Gnomad AMR exome AF: 0.00483

Gnomad ASJ exome AF: 0.00946

Gnomad EAS exome AF: 0.00763

Gnomad FIN exome AF: 0.000622

Gnomad NFE exome AF: 0.00402

Gnomad OTH exome AF: 0.00322

GnomAD4 exome AF: 0.00179 AC: 1893 AN: 1056000 Hom.: 0 AF XY: 0.00197 AC XY: 1014 AN XY: 515630

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

African (AFR) AF: 0.00852 AC: 192 AN: 22532

American (AMR) AF: 0.00477 AC: 52 AN: 10900

Ashkenazi Jewish (ASJ) AF: 0.00492 AC: 78 AN: 15848

East Asian (EAS) AF: 0.00221 AC: 56 AN: 25384

South Asian (SAS) AF: 0.00534 AC: 213 AN: 39912

European-Finnish (FIN) AF: 0.00232 AC: 82 AN: 35382

Middle Eastern (MID) AF: 0.00274 AC: 10 AN: 3654

European-Non Finnish (NFE) AF: 0.00130 AC: 1121 AN: 859328

Other (OTH) AF: 0.00207 AC: 89 AN: 43060

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.000258 AC: 34 AN: 131684 Hom.: 0 Cov.: 0 AF XY: 0.000222 AC XY: 14 AN XY: 62968

African (AFR) AF: 0.000770 AC: 28 AN: 36360

American (AMR) AF: 0.0000752 AC: 1 AN: 13296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3196

East Asian (EAS) AF: 0.00 AC: 0 AN: 4530

South Asian (SAS) AF: 0.00 AC: 0 AN: 3998

European-Finnish (FIN) AF: 0.000151 AC: 1 AN: 6608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 248

European-Non Finnish (NFE) AF: 0.0000493 AC: 3 AN: 60810

Other (OTH) AF: 0.000549 AC: 1 AN: 1820

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493;