rs10208402

chr2-114446340-C-T

Variant summary

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

The NM_020868.6(DPP10):c.60+3502C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,948 control chromosomes in the GnomAD database, including 20,119 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 0.51 (20119 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

Genes affected

DPP10 (HGNC:20823): (dipeptidyl peptidase like 10) This gene encodes a single-pass type II membrane protein that is a member of the S9B family in clan SC of the serine proteases. This protein has no detectable protease activity, most likely due to the absence of the conserved serine residue normally present in the catalytic domain of serine proteases. However, it does bind specific voltage-gated potassium channels and alters their expression and biophysical properties. Mutations in this gene have been associated with asthma. Alternate transcriptional splice variants, encoding different isoforms, have been 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.60+3502C>T		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.60+3502C>T		intron_variant		1	NM_020868.6	A1
DPP10	ENST00000436732.5	c.-163+3502C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77624 AN: 151830 Hom.: 20103 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.571

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.511 AC: 77687 AN: 151948 Hom.: 20119 Cov.: 33 AF XY: 0.507 AC XY: 37621 AN XY: 74240

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.567

Alfa AF: 0.524 Hom.: 42639

Bravo AF: 0.513

Asia WGS AF: 0.418 AC: 1453 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10208402; hg19: chr2-115203917;