rs2420815

chr2-115320866-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.175+11513C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,898 control chromosomes in the GnomAD database, including 35,736 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 0.68 (35736 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.175+11513C>T		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.175+11513C>T		intron_variant		1	NM_020868.6	A1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103167 AN: 151782 Hom.: 35722 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.680 AC: 103228 AN: 151898 Hom.: 35736 Cov.: 32 AF XY: 0.681 AC XY: 50524 AN XY: 74220

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.675

Alfa AF: 0.720 Hom.: 18255

Bravo AF: 0.673

Asia WGS AF: 0.732 AC: 2545 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.67
Dann	Benign	0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2420815; hg19: chr2-116078442;