13-19467353-TAAAAAAAA-TAAAAAAA

Position:

• chr13-19467353-TAAAAAAAA-TAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001395978.1(TPTE2):​c.393-10del variant causes a splice polypyrimidine tract, 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 0.73 (36243 hom., cov: 0)
  • Exomes 𝑓: 0.47 (4727 hom.)
  • Failed GnomAD Quality Control
• Consequence: TPTE2 NM_001395978.1 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPTE2	NM_001395978.1	c.393-10del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000697147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPTE2	ENST00000697147.1	c.393-10del		splice_polypyrimidine_tract_variant, intron_variant			NM_001395978.1	P2

Frequencies

GnomAD3 genomes AF: 0.727 AC: 95728 AN: 131632 Hom.: 36259 Cov.: 0

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.758

GnomAD3 exomes AF: 0.382 AC: 12486 AN: 32670 Hom.: 179 AF XY: 0.373 AC XY: 6306 AN XY: 16922

Gnomad AFR exome AF: 0.251

Gnomad AMR exome AF: 0.351

Gnomad ASJ exome AF: 0.341

Gnomad EAS exome AF: 0.388

Gnomad SAS exome AF: 0.314

Gnomad FIN exome AF: 0.437

Gnomad NFE exome AF: 0.389

Gnomad OTH exome AF: 0.378

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.470 AC: 496500 AN: 1056792 Hom.: 4727 Cov.: 0 AF XY: 0.468 AC XY: 241365 AN XY: 516176

Gnomad4 AFR exome AF: 0.337

Gnomad4 AMR exome AF: 0.423

Gnomad4 ASJ exome AF: 0.433

Gnomad4 EAS exome AF: 0.473

Gnomad4 SAS exome AF: 0.429

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.478

Gnomad4 OTH exome AF: 0.463

GnomAD4 genome AF: 0.727 AC: 95696 AN: 131636 Hom.: 36243 Cov.: 0 AF XY: 0.728 AC XY: 45839 AN XY: 62940

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493;