rs10496474

Variant names:

• chr2-114778111-G-A
• rs10496474
• NM_020868.6:c.60+335273G>A

Variant summary

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

The NM_020868.6(DPP10):​c.60+335273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 151,888 control chromosomes in the GnomAD database, including 906 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 0.090 (906 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.60+335273G>A		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.60+335273G>A		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000409163.5	c.-91+314685G>A		intron_variant	Intron 2 of 26	2		ENSP00000387038.1
DPP10	ENST00000436732.5	c.-162-272037G>A		intron_variant	Intron 1 of 4	4		ENSP00000391092.1
DPP10	ENST00000461250.5	n.654+70937G>A		intron_variant	Intron 3 of 7	2

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13582 AN: 151770 Hom.: 899 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.0155

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0897 AC: 13621 AN: 151888 Hom.: 906 Cov.: 32 AF XY: 0.0888 AC XY: 6596 AN XY: 74256

African (AFR) AF: 0.171 AC: 7098 AN: 41438

American (AMR) AF: 0.0770 AC: 1174 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0523 AC: 181 AN: 3460

East Asian (EAS) AF: 0.0155 AC: 80 AN: 5164

South Asian (SAS) AF: 0.109 AC: 523 AN: 4804

European-Finnish (FIN) AF: 0.0472 AC: 499 AN: 10568

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0559 AC: 3794 AN: 67900

Other (OTH) AF: 0.0791 AC: 167 AN: 2112

Alfa AF: 0.0735 Hom.: 164

Bravo AF: 0.0923

Asia WGS AF: 0.0810 AC: 281 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.30
PhyloP100		-0.16
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: rs10496474; hg19: chr2-115535688;