2-114456098-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+13260T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,008 control chromosomes in the GnomAD database, including 34,706 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 0.67 (34706 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.60+13260T>C		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.60+13260T>C		intron_variant		1	NM_020868.6	A1
DPP10	ENST00000436732.5	c.-163+13260T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102372 AN: 151890 Hom.: 34677 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.674 AC: 102443 AN: 152008 Hom.: 34706 Cov.: 31 AF XY: 0.674 AC XY: 50087 AN XY: 74302

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.686

Alfa AF: 0.684 Hom.: 68856

Bravo AF: 0.673

Asia WGS AF: 0.624 AC: 2171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6737251; hg19: chr2-115213675;