13-19467353-TAAAAAAAA-TAAAAAAAAAA

Variant names:

• chr13-19467353-T-TAA
• rs71092363
• NM_001395978.1:c.393-11_393-10dupTT

Variant summary

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

The NM_001395978.1(TPTE2):​c.393-11_393-10dupTT 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 0.000023 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00021 (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.393-11_393-10dupTT		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_393-9insTT		intron_variant	Intron 9 of 22		NM_001395978.1	ENSP00000513136.1

Frequencies

GnomAD3 genomes AF: 0.0000228 AC: 3 AN: 131678 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000276

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000329

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000673 AC: 22 AN: 32670 AF XY: 0.000591

Gnomad AFR exome AF: 0.00109

Gnomad AMR exome AF: 0.00241

Gnomad ASJ exome AF: 0.000789

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000622

Gnomad NFE exome AF: 0.000555

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000215 AC: 228 AN: 1061548 Hom.: 0 Cov.: 0 AF XY: 0.000218 AC XY: 113 AN XY: 518520

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

African (AFR) AF: 0.000264 AC: 6 AN: 22688

American (AMR) AF: 0.000545 AC: 6 AN: 11010

Ashkenazi Jewish (ASJ) AF: 0.000376 AC: 6 AN: 15970

East Asian (EAS) AF: 0.0000780 AC: 2 AN: 25636

South Asian (SAS) AF: 0.000497 AC: 20 AN: 40252

European-Finnish (FIN) AF: 0.000281 AC: 10 AN: 35576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3672

European-Non Finnish (NFE) AF: 0.000193 AC: 167 AN: 863392

Other (OTH) AF: 0.000254 AC: 11 AN: 43352

⚠️ 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: 0.0000228 AC: 3 AN: 131678 Hom.: 0 Cov.: 0 AF XY: 0.0000477 AC XY: 3 AN XY: 62932

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

African (AFR) AF: 0.0000276 AC: 1 AN: 36296

American (AMR) AF: 0.00 AC: 0 AN: 13286

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4548

South Asian (SAS) AF: 0.00 AC: 0 AN: 4022

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.0000329 AC: 2 AN: 60822

Other (OTH) AF: 0.00 AC: 0 AN: 1810

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.001100), which strongly suggests a high chance of mosaicism in these individuals.

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

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

Other links and lift over

dbSNP: rs71092363; hg19: chr13-20041493;