2-115444847-A-G

Variant names:

• chr2-115444847-A-G
• rs717522
• NM_020868.6:c.272-54663A>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.272-54663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,188 control chromosomes in the GnomAD database, including 3,236 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 (3236 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	NM_020868.6	MANE Select	c.272-54663A>G		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.323-54663A>G		intron	N/A	NP_001308834.2
	DPP10	NM_001178034.1		c.284-54663A>G		intron	N/A	NP_001171505.1	Q8N608

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.272-54663A>G		intron	N/A	ENSP00000386565.1	Q8N608-1
	DPP10	ENST00000393147.6	TSL:1	c.284-54663A>G		intron	N/A	ENSP00000376855.2	Q8N608-3
	DPP10	ENST00000310323.12	TSL:1	c.251-54663A>G		intron	N/A	ENSP00000309066.8	Q8N608-2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21162 AN: 152070 Hom.: 3233 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.139 AC: 21191 AN: 152188 Hom.: 3236 Cov.: 32 AF XY: 0.137 AC XY: 10183 AN XY: 74412

African (AFR) AF: 0.369 AC: 15327 AN: 41496

American (AMR) AF: 0.0789 AC: 1206 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1236 AN: 5160

South Asian (SAS) AF: 0.102 AC: 493 AN: 4824

European-Finnish (FIN) AF: 0.0315 AC: 335 AN: 10620

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0301 AC: 2046 AN: 68006

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0347 Hom.: 73

Bravo AF: 0.154

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.70
PhyloP100		-0.93
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: rs717522; hg19: chr2-116202423;