rs10496506

Positions:

• chr2-115779186-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.1361+1352T>C		intron_variant		ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.1361+1352T>C		intron_variant		1	NM_020868.6	ENSP00000386565	A1
DPP10	ENST00000310323.12	c.1340+1352T>C		intron_variant		1		ENSP00000309066
DPP10	ENST00000393147.6	c.1373+1352T>C		intron_variant		1		ENSP00000376855	P3
DPP10	ENST00000409163.5	c.1211+1352T>C		intron_variant		2		ENSP00000387038

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

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0866

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.5
DANN	Benign	0.85

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: rs10496506; hg19: chr2-116536762;