2-115383824-T-C

Variant names:

• chr2-115383824-T-C
• rs10167944
• NM_020868.6:c.271+39912T>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.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
• Publications: 2 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=-0.85).
• 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 rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.271+39912T>C		intron_variant	Intron 3 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.271+39912T>C		intron_variant	Intron 3 of 25	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

African (AFR) AF: 0.595 AC: 24681 AN: 41468

American (AMR) AF: 0.754 AC: 11524 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3468

East Asian (EAS) AF: 0.701 AC: 3616 AN: 5156

South Asian (SAS) AF: 0.658 AC: 3176 AN: 4826

European-Finnish (FIN) AF: 0.694 AC: 7339 AN: 10576

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48739 AN: 67992

Other (OTH) AF: 0.667 AC: 1412 AN: 2116

Alfa AF: 0.694 Hom.: 6404

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
PhyloP100		0.29
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: rs10167944; hg19: chr2-116141400;