rs1375144

chr2-115483610-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):c.272-15900G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,824 control chromosomes in the GnomAD database, including 25,036 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 0.56 (25036 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.272-15900G>A		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.272-15900G>A		intron_variant		1	NM_020868.6	A1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84882 AN: 151708 Hom.: 25025 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.559 AC: 84927 AN: 151824 Hom.: 25036 Cov.: 31 AF XY: 0.553 AC XY: 41051 AN XY: 74178

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.576

Alfa AF: 0.649 Hom.: 59553

Bravo AF: 0.545

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.42
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1375144; hg19: chr2-116241186;