rs11670570

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000646573.2(DPP9):​c.*2155T>C variant causes a 3 prime UTR, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,324 control chromosomes in the GnomAD database, including 6,480 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 0.27 ( 6480 hom., cov: 30)

Consequence

DPP9
ENST00000646573.2 3_prime_UTR, NMD_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DPP9ENST00000646573.2 linkuse as main transcriptc.*2155T>C 3_prime_UTR_variant, NMD_transcript_variant 21/21

Frequencies

GnomAD3 genomes
AF:
0.274
AC:
41476
AN:
151204
Hom.:
6465
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.426
Gnomad AMI
AF:
0.397
Gnomad AMR
AF:
0.250
Gnomad ASJ
AF:
0.332
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.289
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.326
Gnomad NFE
AF:
0.211
Gnomad OTH
AF:
0.297
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.274
AC:
41534
AN:
151324
Hom.:
6480
Cov.:
30
AF XY:
0.272
AC XY:
20105
AN XY:
73924
show subpopulations
Gnomad4 AFR
AF:
0.426
Gnomad4 AMR
AF:
0.250
Gnomad4 ASJ
AF:
0.332
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.288
Gnomad4 FIN
AF:
0.142
Gnomad4 NFE
AF:
0.211
Gnomad4 OTH
AF:
0.294
Alfa
AF:
0.233
Hom.:
5721
Bravo
AF:
0.288
Asia WGS
AF:
0.225
AC:
787
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.9
DANN
Benign
0.77

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11670570; hg19: chr19-4674799; API