rs11670570

Variant names:

• chr19-4674787-A-G
• rs11670570
• ENST00000646573.2:n.*2155T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646573.2(DPP9):​n.*2155T>C variant causes a non coding transcript exon 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 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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]

ACMG classification

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP9	ENST00000646573.2	n.*2155T>C		non_coding_transcript_exon_variant	Exon 21 of 21			ENSP00000496196.2
DPP9	ENST00000646573.2	n.*2155T>C		3_prime_UTR_variant	Exon 21 of 21			ENSP00000496196.2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41476 AN: 151204 Hom.: 6465 Cov.: 30

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

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

Other links and lift over

dbSNP: rs11670570; hg19: chr19-4674799;