Genetic Variant DPP9:c.56+517_56+524delTTTATTTA (chr19-4719326-TTAAATAAA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_139159.5(DPP9):c.56+517_56+524delTTTATTTA variant causes a 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_139159.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.181

Publications

1 publications found

Variant links:

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 Gene-Disease associations (from GenCC):

hatipoglu immunodeficiency syndrome
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

DPP9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DPP9	NM_139159.5 link	c.56+517_56+524delTTTATTTA		intron_variant	Intron 3 of 21	ENST00000262960.14	NP_631898.3	Q86TI2-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP9	ENST00000262960.14 link	c.56+517_56+524delTTTATTTA		intron_variant	Intron 3 of 21	1	NM_139159.5	ENSP00000262960.8		Q86TI2-2

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

41033

AN:

141652

Hom.:

6410

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.290

AC:

41058

AN:

141748

Hom.:

6416

Cov.:

AF XY:

0.287

AC XY:

19628

AN XY:

68406

show subpopulations

African (AFR)

AF:

0.186

AC:

7044

AN:

37892

American (AMR)

AF:

0.320

AC:

4520

AN:

14146

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

835

AN:

3374

East Asian (EAS)

AF:

0.135

AC:

640

AN:

4724

South Asian (SAS)

AF:

0.208

AC:

865

AN:

4164

European-Finnish (FIN)

AF:

0.351

AC:

3076

AN:

8758

Middle Eastern (MID)

AF:

0.291

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.351

AC:

23057

AN:

65598

Other (OTH)

AF:

0.293

AC:

565

AN:

1928

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1271

2543

3814

5086

6357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.264

Hom.:

308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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chr19-4719326-TTAAATAAA-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over