19-4719326-TTAAATAAATAAATAAATAAATAAA-TTAAATAAATAAATAAA

Position:

• chr19-4719326-TTAAATAAATAAATAAATAAATAAA-TTAAATAAATAAATAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001384624.1(DPP9):​c.-153-10_-153-3delTTTATTTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 141,760 control chromosomes in the GnomAD database, including 6,416 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.29 (6416 hom., cov: 0)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: DPP9 NM_001384624.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

DPP9 (HGNC:18648): (dipeptidyl peptidase 9) This gene encodes a protein that is a member of the S9B family in clan SC of the serine proteases. The protein has been shown to have post-proline dipeptidyl aminopeptidase activity, cleaving Xaa-Pro dipeptides from the N-termini of proteins. Although the activity of this protein is similar to that of dipeptidyl peptidase 4 (DPP4), it does not appear to be membrane bound. In general, dipeptidyl peptidases appear to be involved in the regulation of the activity of their substrates and have been linked to a variety of diseases including type 2 diabetes, obesity and cancer. Several transcript variants of this gene have been described but not fully characterized. [provided by RefSeq, Jul 2008]

DPP9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP9	NM_139159.5	c.56+517_56+524delTTTATTTA		intron_variant		ENST00000262960.14	NP_631898.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP9	ENST00000262960.14	c.56+517_56+524delTTTATTTA		intron_variant		1	NM_139159.5	ENSP00000262960.8

Frequencies

GnomAD3 genomes AF: 0.290 AC: 41033 AN: 141652 Hom.: 6410 Cov.: 0

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.284

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.250 AC: 3 AN: 12 Hom.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.300

GnomAD4 genome AF: 0.290 AC: 41058 AN: 141748 Hom.: 6416 Cov.: 0 AF XY: 0.287 AC XY: 19628 AN XY: 68406

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3059236; hg19: chr19-4719338;