13-19467353-TAAAAAAAA-TAAAAAAAAA

Variant names:

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

Variant summary

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

The NM_001395978.1(TPTE2):​c.393-10dupT 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 0.0011 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0041 (0 hom.)
• 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: 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.393-10dupT		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.393-10_393-9insT		intron_variant	Intron 9 of 22		NM_001395978.1	ENSP00000513136.1

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

GnomAD2 exomes AF: 0.00618 AC: 202 AN: 32670 AF XY: 0.00597

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 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

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

African (AFR) AF: 0.00947 AC: 214 AN: 22598

American (AMR) AF: 0.00528 AC: 58 AN: 10982

Ashkenazi Jewish (ASJ) AF: 0.00465 AC: 74 AN: 15906

East Asian (EAS) AF: 0.00282 AC: 72 AN: 25560

South Asian (SAS) AF: 0.00414 AC: 166 AN: 40118

European-Finnish (FIN) AF: 0.00649 AC: 230 AN: 35418

Middle Eastern (MID) AF: 0.00764 AC: 28 AN: 3666

European-Non Finnish (NFE) AF: 0.00375 AC: 3224 AN: 859754

Other (OTH) AF: 0.00505 AC: 218 AN: 43198

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

African (AFR) AF: 0.00179 AC: 65 AN: 36358

American (AMR) AF: 0.00165 AC: 22 AN: 13296

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

East Asian (EAS) AF: 0.00155 AC: 7 AN: 4528

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

European-Finnish (FIN) AF: 0.000454 AC: 3 AN: 6608

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

European-Non Finnish (NFE) AF: 0.000608 AC: 37 AN: 60808

Other (OTH) AF: 0.00330 AC: 6 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		0.0

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

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493;