2-115383824-T-C

Position:

• chr2-115383824-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.271+39912T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,090 control chromosomes in the GnomAD database, including 35,358 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 (35358 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294

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]

DPP10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.271+39912T>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.271+39912T>C		intron_variant		1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103158 AN: 151970 Hom.: 35341 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.679 AC: 103228 AN: 152090 Hom.: 35358 Cov.: 33 AF XY: 0.678 AC XY: 50401 AN XY: 74348

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.667

Alfa AF: 0.696 Hom.: 6262

Bravo AF: 0.679

Asia WGS AF: 0.683 AC: 2362 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.76

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: rs10167944; hg19: chr2-116141400;