rs1396932

Variant names:

• chr2-114984171-A-C
• rs1396932
• NM_020868.6:c.61-325068A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.61-325068A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,074 control chromosomes in the GnomAD database, including 21,766 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 0.53 (21766 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.61-325068A>C		intron_variant	Intron 1 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.61-325068A>C		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000409163.5	c.-90-325068A>C		intron_variant	Intron 2 of 26	2		ENSP00000387038.1
DPP10	ENST00000436732.5	c.-162-65977A>C		intron_variant	Intron 1 of 4	4		ENSP00000391092.1
DPP10	ENST00000461250.5	n.654+276997A>C		intron_variant	Intron 3 of 7	2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80938 AN: 151956 Hom.: 21761 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.533 AC: 80983 AN: 152074 Hom.: 21766 Cov.: 33 AF XY: 0.526 AC XY: 39104 AN XY: 74330

African (AFR) AF: 0.500 AC: 20734 AN: 41454

American (AMR) AF: 0.549 AC: 8394 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3468

East Asian (EAS) AF: 0.607 AC: 3135 AN: 5164

South Asian (SAS) AF: 0.524 AC: 2527 AN: 4826

European-Finnish (FIN) AF: 0.455 AC: 4811 AN: 10574

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37912 AN: 67976

Other (OTH) AF: 0.495 AC: 1048 AN: 2116

Alfa AF: 0.544 Hom.: 11686

Bravo AF: 0.539

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.67
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1396932; hg19: chr2-115741748;