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_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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384624.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DPP9	NM_139159.5	MANE Select	c.56+517_56+524delTTTATTTA	intron	N/A	NP_631898.3
DPP9	NM_001384611.1		c.56+517_56+524delTTTATTTA	intron	N/A	NP_001371540.1
DPP9	NM_001384612.1		c.56+517_56+524delTTTATTTA	intron	N/A	NP_001371541.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DPP9	ENST00000262960.14	TSL:1 MANE Select	c.56+517_56+524delTTTATTTA	intron	N/A	ENSP00000262960.8
DPP9	ENST00000600621.6	TSL:4	c.56+517_56+524delTTTATTTA	intron	N/A	ENSP00000472549.2
DPP9	ENST00000601130.6	TSL:4	c.56+517_56+524delTTTATTTA	intron	N/A	ENSP00000471629.2

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.264

Hom.:

308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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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19-4719326-TTAAATAAATAAATAAATAAATAAA-TTAAATAAATAAATAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over