chr2-114451104-T-C

Position:

• chr2-114451104-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.8).
• 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/exons	MANE	UniProt
DPP10	NM_020868.6	c.60+8266T>C		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.60+8266T>C		intron_variant		1	NM_020868.6	A1
DPP10	ENST00000436732.5	c.-163+8266T>C		intron_variant		4

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

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.0590

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.345

Alfa AF: 0.371 Hom.: 14127

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10192393; hg19: chr2-115208681;