NM_020868.6:c.60+179836T>G

Variant names:

• chr2-114622674-T-G
• rs10186236
• NM_020868.6:c.60+179836T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.60+179836T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,968 control chromosomes in the GnomAD database, including 8,446 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 0.29 (8446 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.60+179836T>G		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.60+179836T>G		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000409163.5	c.-91+159248T>G		intron_variant	Intron 2 of 26	2		ENSP00000387038.1
DPP10	ENST00000436732.5	c.-163+179836T>G		intron_variant	Intron 1 of 4	4		ENSP00000391092.1
DPP10	ENST00000461250.5	n.597-84443T>G		intron_variant	Intron 2 of 7	2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44577 AN: 151850 Hom.: 8406 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.294 AC: 44683 AN: 151968 Hom.: 8446 Cov.: 32 AF XY: 0.289 AC XY: 21479 AN XY: 74282

African (AFR) AF: 0.546 AC: 22636 AN: 41426

American (AMR) AF: 0.223 AC: 3407 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3466

East Asian (EAS) AF: 0.312 AC: 1604 AN: 5146

South Asian (SAS) AF: 0.157 AC: 759 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1780 AN: 10600

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13175 AN: 67952

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.226 Hom.: 17869

Bravo AF: 0.308

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.48
PhyloP100		-0.67
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: rs10186236; hg19: chr2-115380251;