chr13-19467353-T-TA

Position:

• chr13-19467353-T-TA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001395978.1(TPTE2):​c.393-10_393-9insT 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 0.0011 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0041 (0 hom.)
• 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPTE2	NM_001395978.1	c.393-10_393-9insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000697147.1	NP_001382907.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPTE2	ENST00000697147.1	c.393-10_393-9insT		splice_polypyrimidine_tract_variant, intron_variant			NM_001395978.1	ENSP00000513136	P2

Frequencies

GnomAD3 genomes AF: 0.00105 AC: 138 AN: 131676 Hom.: 0 Cov.: 0

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

GnomAD3 exomes AF: 0.00618 AC: 202 AN: 32670 Hom.: 0 AF XY: 0.00597 AC XY: 101 AN XY: 16922

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 SAS exome AF: 0.00435

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.: 0 Cov.: 0 AF XY: 0.00412 AC XY: 2126 AN XY: 516382

Gnomad4 AFR exome AF: 0.00947

Gnomad4 AMR exome AF: 0.00528

Gnomad4 ASJ exome AF: 0.00465

Gnomad4 EAS exome AF: 0.00282

Gnomad4 SAS exome AF: 0.00414

Gnomad4 FIN exome AF: 0.00649

Gnomad4 NFE exome AF: 0.00375

Gnomad4 OTH exome AF: 0.00505

GnomAD4 genome AF: 0.00106 AC: 140 AN: 131678 Hom.: 0 Cov.: 0 AF XY: 0.00116 AC XY: 73 AN XY: 62962

Gnomad4 AFR AF: 0.00179

Gnomad4 AMR AF: 0.00165

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000454

Gnomad4 NFE AF: 0.000608

Gnomad4 OTH AF: 0.00330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493;