rs661577

chr13-102673963-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330588.2(TPP2):c.3372-320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,212 control chromosomes in the GnomAD database, including 50,803 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (50803 hom., cov: 32)
• Consequence: TPP2 NM_001330588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

Genes affected

TPP2 (HGNC:12016): (tripeptidyl peptidase 2) This gene encodes a mammalian peptidase that, at neutral pH, removes tripeptides from the N terminus of longer peptides. The protein has a specialized function that is essential for some MHC class I antigen presentation. The protein is a high molecular mass serine exopeptidase; the amino acid sequence surrounding the serine residue at the active site is similar to the peptidases of the subtilisin class rather than the trypsin class. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPP2	NM_001330588.2	c.3372-320G>A		intron_variant		ENST00000376052.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPP2	ENST00000376052.5	c.3372-320G>A		intron_variant		5	NM_001330588.2	A1

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123689 AN: 152094 Hom.: 50762 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.833

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.813 AC: 123781 AN: 152212 Hom.: 50803 Cov.: 32 AF XY: 0.810 AC XY: 60250 AN XY: 74420

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.836

Alfa AF: 0.797 Hom.: 22980

Bravo AF: 0.813

Asia WGS AF: 0.767 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.64
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs661577; hg19: chr13-103326313;