2-115313789-C-T

Position:

• chr2-115313789-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.175+4436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,260 control chromosomes in the GnomAD database, including 61,960 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 0.90 (61960 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.175+4436C>T		intron_variant		ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.175+4436C>T		intron_variant		1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137098 AN: 152142 Hom.: 61908 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.901 AC: 137211 AN: 152260 Hom.: 61960 Cov.: 33 AF XY: 0.899 AC XY: 66931 AN XY: 74434

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.877

Alfa AF: 0.894 Hom.: 32159

Bravo AF: 0.898

Asia WGS AF: 0.815 AC: 2828 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.19

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: rs6542256; hg19: chr2-116071365;