2-114479255-T-C

Variant names:

• chr2-114479255-T-C
• rs7580359
• NM_020868.6:c.60+36417T>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.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
• 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=-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 rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.60+36417T>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.60+36417T>C		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000409163.5	c.-91+15829T>C		intron_variant	Intron 2 of 26	2		ENSP00000387038.1
DPP10	ENST00000436732.5	c.-163+36417T>C		intron_variant	Intron 1 of 4	4		ENSP00000391092.1
DPP10	ENST00000461250.5	n.596+15829T>C		intron_variant	Intron 2 of 7	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

African (AFR) AF: 0.639 AC: 26488 AN: 41444

American (AMR) AF: 0.664 AC: 10129 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3468

East Asian (EAS) AF: 0.712 AC: 3676 AN: 5166

South Asian (SAS) AF: 0.482 AC: 2320 AN: 4814

European-Finnish (FIN) AF: 0.674 AC: 7114 AN: 10554

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44929 AN: 67902

Other (OTH) AF: 0.652 AC: 1375 AN: 2110

Alfa AF: 0.641 Hom.: 3860

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
PhyloP100		0.41
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: rs7580359; hg19: chr2-115236832;