rs10192393

Variant names:

• chr2-114451104-T-C
• rs10192393
• NM_020868.6:c.60+8266T>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.60+8266T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,824 control chromosomes in the GnomAD database, including 8,797 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 0.33 (8797 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.60+8266T>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.60+8266T>C		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000436732.5	c.-163+8266T>C		intron_variant	Intron 1 of 4	4		ENSP00000391092.1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50738 AN: 151706 Hom.: 8796 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.334 AC: 50761 AN: 151824 Hom.: 8797 Cov.: 31 AF XY: 0.329 AC XY: 24394 AN XY: 74198

African (AFR) AF: 0.323 AC: 13391 AN: 41436

American (AMR) AF: 0.299 AC: 4563 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1253 AN: 3462

East Asian (EAS) AF: 0.0590 AC: 305 AN: 5166

South Asian (SAS) AF: 0.360 AC: 1734 AN: 4814

European-Finnish (FIN) AF: 0.286 AC: 3014 AN: 10530

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25300 AN: 67860

Other (OTH) AF: 0.345 AC: 725 AN: 2104

Alfa AF: 0.368 Hom.: 17548

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.88
PhyloP100		0.70
Mutation Taster		=8/92	disease causing (long InDel)

Splicing

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

Other links and lift over

dbSNP: rs10192393; hg19: chr2-115208681;