chr2-115124275-A-G

Variant names:

• chr2-115124275-A-G
• rs7579207
• NM_020868.6:c.61-184964A>G

Variant summary

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

The NM_020868.6(DPP10):​c.61-184964A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,066 control chromosomes in the GnomAD database, including 40,099 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 0.72 (40099 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

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.61-184964A>G		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.112-184964A>G		intron	N/A	NP_001308834.2
	DPP10	NM_001178037.3		c.48+59470A>G		intron	N/A	NP_001171508.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.61-184964A>G		intron	N/A	ENSP00000386565.1
	DPP10	ENST00000409163.5	TSL:2	c.-90-184964A>G		intron	N/A	ENSP00000387038.1
	DPP10	ENST00000393146.6	TSL:5	c.48+59470A>G		intron	N/A	ENSP00000376854.2

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109814 AN: 151948 Hom.: 40052 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.723 AC: 109924 AN: 152066 Hom.: 40099 Cov.: 32 AF XY: 0.727 AC XY: 54011 AN XY: 74326

African (AFR) AF: 0.752 AC: 31171 AN: 41464

American (AMR) AF: 0.729 AC: 11137 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2616 AN: 3472

East Asian (EAS) AF: 0.982 AC: 5057 AN: 5152

South Asian (SAS) AF: 0.624 AC: 3009 AN: 4820

European-Finnish (FIN) AF: 0.787 AC: 8339 AN: 10592

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46387 AN: 67972

Other (OTH) AF: 0.703 AC: 1485 AN: 2112

Alfa AF: 0.694 Hom.: 62010

Bravo AF: 0.725

Asia WGS AF: 0.799 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.43
PhyloP100		-1.2
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: rs7579207; hg19: chr2-115881852;