NM_001395978.1:c.393-10delT

Variant names:

• chr13-19467353-TA-T
• rs71092363
• NM_001395978.1:c.393-10delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001395978.1(TPTE2):​c.393-10delT 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 0.73 (36243 hom., cov: 0)
  • Exomes 𝑓: 0.47 (4727 hom.)
  • Failed GnomAD Quality Control
• Consequence: TPTE2 NM_001395978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• 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: Benign. The variant received -8 ACMG points.

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

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTE2	ENST00000697147.1	MANE Select	c.393-10delT		intron	N/A	ENSP00000513136.1
	TPTE2	ENST00000390680.2	TSL:1	c.282-1790delT		intron	N/A	ENSP00000375098.2
	TPTE2	ENST00000696858.2		c.393-10delT		intron	N/A	ENSP00000512931.1

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

GnomAD2 exomes AF: 0.382 AC: 12486 AN: 32670 AF XY: 0.373

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 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

African (AFR) AF: 0.337 AC: 7457 AN: 22156

American (AMR) AF: 0.423 AC: 4646 AN: 10972

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 6861 AN: 15852

East Asian (EAS) AF: 0.473 AC: 12102 AN: 25600

South Asian (SAS) AF: 0.429 AC: 17206 AN: 40098

European-Finnish (FIN) AF: 0.428 AC: 15071 AN: 35208

Middle Eastern (MID) AF: 0.450 AC: 1634 AN: 3634

European-Non Finnish (NFE) AF: 0.478 AC: 411534 AN: 860142

Other (OTH) AF: 0.463 AC: 19989 AN: 43130

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

African (AFR) AF: 0.450 AC: 16315 AN: 36280

American (AMR) AF: 0.829 AC: 11026 AN: 13296

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2507 AN: 3192

East Asian (EAS) AF: 0.889 AC: 4029 AN: 4530

South Asian (SAS) AF: 0.846 AC: 3379 AN: 3996

European-Finnish (FIN) AF: 0.799 AC: 5308 AN: 6642

Middle Eastern (MID) AF: 0.706 AC: 175 AN: 248

European-Non Finnish (NFE) AF: 0.837 AC: 50903 AN: 60820

Other (OTH) AF: 0.757 AC: 1374 AN: 1814

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493;