2-115115219-C-T

Position:

• chr2-115115219-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.61-194020C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,858 control chromosomes in the GnomAD database, including 15,919 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 0.45 (15919 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.61-194020C>T		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.61-194020C>T		intron_variant		1	NM_020868.6	A1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68910 AN: 151740 Hom.: 15901 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.454 AC: 68987 AN: 151858 Hom.: 15919 Cov.: 31 AF XY: 0.457 AC XY: 33925 AN XY: 74226

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.438

Alfa AF: 0.420 Hom.: 27336

Bravo AF: 0.463

Asia WGS AF: 0.549 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4277531; hg19: chr2-115872796; COSMIC: COSV67714047;