rs17823623

Variant names:

• chr2-115367077-G-C
• rs17823623
• NM_020868.6:c.271+23165G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_020868.6(DPP10):​c.271+23165G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 152,138 control chromosomes in the GnomAD database, including 61 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 0.025 (61 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 2 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=-0.94).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0252 (3828/152138) while in subpopulation AMR AF = 0.0464 (707/15252). AF 95% confidence interval is 0.0435. There are 61 homozygotes in GnomAd4. There are 1809 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 61 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020868.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	NM_020868.6	MANE Select	c.271+23165G>C		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.322+23165G>C		intron	N/A	NP_001308834.2
	DPP10	NM_001178034.1		c.283+23165G>C		intron	N/A	NP_001171505.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.271+23165G>C		intron	N/A	ENSP00000386565.1
	DPP10	ENST00000393147.6	TSL:1	c.283+23165G>C		intron	N/A	ENSP00000376855.2
	DPP10	ENST00000310323.12	TSL:1	c.250+23165G>C		intron	N/A	ENSP00000309066.8

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3831 AN: 152020 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.00684

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0252 AC: 3828 AN: 152138 Hom.: 61 Cov.: 32 AF XY: 0.0243 AC XY: 1809 AN XY: 74390

African (AFR) AF: 0.00682 AC: 283 AN: 41520

American (AMR) AF: 0.0464 AC: 707 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0333 AC: 161 AN: 4828

European-Finnish (FIN) AF: 0.0193 AC: 205 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0338 AC: 2300 AN: 67960

Other (OTH) AF: 0.0299 AC: 63 AN: 2110

Alfa AF: 0.0283 Hom.: 7

Bravo AF: 0.0277

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.51
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs17823623; hg19: chr2-116124653;