2-115329056-A-T

Variant summary

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

The NM_020868.6(DPP10):c.176-14761A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,894 control chromosomes in the GnomAD database, including 37,338 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 0.70 (37338 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.176-14761A>T		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.176-14761A>T		intron_variant		1	NM_020868.6	A1

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105672 AN: 151778 Hom.: 37311 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.696 AC: 105751 AN: 151894 Hom.: 37338 Cov.: 32 AF XY: 0.696 AC XY: 51647 AN XY: 74236

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.687

Alfa AF: 0.719 Hom.: 4938

Bravo AF: 0.690

Asia WGS AF: 0.743 AC: 2582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.0
Dann	Benign	0.40

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: rs925848; hg19: chr2-116086632;