2-114479255-T-C

Position:

• chr2-114479255-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+36417T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,918 control chromosomes in the GnomAD database, including 32,363 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 0.65 (32363 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.60+36417T>C		intron_variant		ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.60+36417T>C		intron_variant		1	NM_020868.6	ENSP00000386565	A1
DPP10	ENST00000409163.5	c.-91+15829T>C		intron_variant		2		ENSP00000387038
DPP10	ENST00000436732.5	c.-163+36417T>C		intron_variant		4		ENSP00000391092
DPP10	ENST00000461250.5	n.596+15829T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98851 AN: 151800 Hom.: 32338 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.651 AC: 98920 AN: 151918 Hom.: 32363 Cov.: 31 AF XY: 0.652 AC XY: 48376 AN XY: 74234

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.652

Alfa AF: 0.643 Hom.: 3716

Bravo AF: 0.652

Asia WGS AF: 0.602 AC: 2078 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7580359; hg19: chr2-115236832;