2-115420003-T-C

Variant names:

• chr2-115420003-T-C
• rs843385
• NM_020868.6:c.271+76091T>C

Variant summary

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

The NM_001321905.3(DPP10):​c.322+76091T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,138 control chromosomes in the GnomAD database, including 2,164 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 0.14 (2164 hom., cov: 32)
• Consequence: DPP10 NM_001321905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321905.3. 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+76091T>C		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.322+76091T>C		intron	N/A	NP_001308834.2
	DPP10	NM_001178034.1		c.283+76091T>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+76091T>C		intron	N/A	ENSP00000386565.1
	DPP10	ENST00000393147.6	TSL:1	c.283+76091T>C		intron	N/A	ENSP00000376855.2
	DPP10	ENST00000310323.12	TSL:1	c.250+76091T>C		intron	N/A	ENSP00000309066.8

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21485 AN: 152020 Hom.: 2159 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.141 AC: 21519 AN: 152138 Hom.: 2164 Cov.: 32 AF XY: 0.141 AC XY: 10460 AN XY: 74372

African (AFR) AF: 0.285 AC: 11838 AN: 41484

American (AMR) AF: 0.0751 AC: 1147 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5170

South Asian (SAS) AF: 0.103 AC: 497 AN: 4816

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10598

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.0885 AC: 6017 AN: 68014

Other (OTH) AF: 0.121 AC: 256 AN: 2110

Alfa AF: 0.0967 Hom.: 1094

Bravo AF: 0.145

Asia WGS AF: 0.0860 AC: 300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.57
PhyloP100		-0.061
Mutation Taster		=100/0	polymorphism (auto)

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: rs843385; hg19: chr2-116177579;