19-4719326-TTAAATAAATAAATAAATAAATAAA-TTAAATAAATAAATAAATAAATAAATAAATAAA

Position:

• chr19-4719326-TTAAATAAATAAATAAATAAATAAA-TTAAATAAATAAATAAATAAATAAATAAATAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001384624.1(DPP9):​c.-153-10_-153-3dupTTTATTTA variant causes a splice region, 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 0.015 (24 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DPP9 NM_001384624.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

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.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0154 (2192/141892) while in subpopulation NFE AF= 0.0178 (1172/65662). AF 95% confidence interval is 0.017. There are 24 homozygotes in gnomad4. There are 1101 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 24 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2194 AN: 141796 Hom.: 24 Cov.: 0

Gnomad AFR AF: 0.00984

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.0392

Gnomad NFE AF: 0.0179

Gnomad OTH AF: 0.0147

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0154 AC: 2192 AN: 141892 Hom.: 24 Cov.: 0 AF XY: 0.0161 AC XY: 1101 AN XY: 68476

Gnomad4 AFR AF: 0.00984

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.0146

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0198

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0150

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;