2-114963319-G-T

Variant names:

• chr2-114963319-G-T
• rs2175176
• NM_020868.6:c.61-345920G>T

Variant summary

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

The NM_020868.6(DPP10):​c.61-345920G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,964 control chromosomes in the GnomAD database, including 15,105 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 0.44 (15105 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.61-345920G>T		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.61-345920G>T		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000409163.5	c.-90-345920G>T		intron_variant	Intron 2 of 26	2		ENSP00000387038.1
DPP10	ENST00000436732.5	c.-162-86829G>T		intron_variant	Intron 1 of 4	4		ENSP00000391092.1
DPP10	ENST00000461250.5	n.654+256145G>T		intron_variant	Intron 3 of 7	2

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66883 AN: 151846 Hom.: 15104 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.440 AC: 66916 AN: 151964 Hom.: 15105 Cov.: 32 AF XY: 0.436 AC XY: 32353 AN XY: 74274

African (AFR) AF: 0.378 AC: 15649 AN: 41434

American (AMR) AF: 0.477 AC: 7277 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3106 AN: 5156

South Asian (SAS) AF: 0.450 AC: 2164 AN: 4812

European-Finnish (FIN) AF: 0.388 AC: 4099 AN: 10554

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31816 AN: 67958

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.458 Hom.: 27789

Bravo AF: 0.445

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.5
DANN	Benign	0.36
PhyloP100		0.37
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: rs2175176; hg19: chr2-115720896;