rs10496493

Positions:

• chr2-115484101-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.272-15409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 148,542 control chromosomes in the GnomAD database, including 3,223 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 0.14 (3223 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.272-15409T>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.272-15409T>C		intron_variant		1	NM_020868.6	ENSP00000386565	A1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21034 AN: 148424 Hom.: 3220 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.142 AC: 21064 AN: 148542 Hom.: 3223 Cov.: 31 AF XY: 0.140 AC XY: 10108 AN XY: 72274

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.0835

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0304

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0935 Hom.: 227

Bravo AF: 0.154

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.50

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: rs10496493; hg19: chr2-116241677;