2-115070916-T-C

Variant names:

• chr2-115070916-T-C
• rs966859
• NM_020868.6:c.61-238323T>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.61-238323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,164 control chromosomes in the GnomAD database, including 2,327 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 0.16 (2327 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 3 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=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.61-238323T>C		intron_variant	Intron 1 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.61-238323T>C		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 25004 AN: 152046 Hom.: 2323 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.165 AC: 25032 AN: 152164 Hom.: 2327 Cov.: 32 AF XY: 0.163 AC XY: 12106 AN XY: 74394

African (AFR) AF: 0.269 AC: 11179 AN: 41496

American (AMR) AF: 0.132 AC: 2020 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 720 AN: 3470

East Asian (EAS) AF: 0.157 AC: 814 AN: 5180

South Asian (SAS) AF: 0.0721 AC: 348 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1069 AN: 10602

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8378 AN: 67986

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.115 Hom.: 670

Bravo AF: 0.170

Asia WGS AF: 0.110 AC: 383 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs966859; hg19: chr2-115828493;