rs10496506

Variant names:

• chr2-115779186-T-C
• rs10496506
• NM_020868.6:c.1361+1352T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.1361+1352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,202 control chromosomes in the GnomAD database, including 657 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 0.080 (657 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020868.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	NM_020868.6	MANE Select	c.1361+1352T>C		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.1412+1352T>C		intron	N/A	NP_001308834.2
	DPP10	NM_001178034.1		c.1373+1352T>C		intron	N/A	NP_001171505.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.1361+1352T>C		intron	N/A	ENSP00000386565.1
	DPP10	ENST00000393147.6	TSL:1	c.1373+1352T>C		intron	N/A	ENSP00000376855.2
	DPP10	ENST00000310323.12	TSL:1	c.1340+1352T>C		intron	N/A	ENSP00000309066.8

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12228 AN: 152084 Hom.: 656 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0804 AC: 12234 AN: 152202 Hom.: 657 Cov.: 33 AF XY: 0.0789 AC XY: 5873 AN XY: 74414

African (AFR) AF: 0.0292 AC: 1213 AN: 41580

American (AMR) AF: 0.0701 AC: 1069 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0650 AC: 314 AN: 4828

European-Finnish (FIN) AF: 0.0982 AC: 1042 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7841 AN: 67958

Other (OTH) AF: 0.0866 AC: 183 AN: 2112

Alfa AF: 0.0944 Hom.: 111

Bravo AF: 0.0747

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.5
DANN	Benign	0.85
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10496506; hg19: chr2-116536762;