NM_020868.6:c.61-350431G>T

Variant names:

• chr2-114958808-G-T
• rs7421482
• NM_020868.6:c.61-350431G>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.61-350431G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,998 control chromosomes in the GnomAD database, including 4,163 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 0.23 (4163 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 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.61-350431G>T		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.111+251634G>T		intron	N/A	NP_001308834.2
	DPP10	NM_001321907.3		c.61-350431G>T		intron	N/A	NP_001308836.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.61-350431G>T		intron	N/A	ENSP00000386565.1
	DPP10	ENST00000409163.5	TSL:2	c.-90-350431G>T		intron	N/A	ENSP00000387038.1
	DPP10	ENST00000436732.5	TSL:4	c.-162-91340G>T		intron	N/A	ENSP00000391092.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34395 AN: 151880 Hom.: 4163 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.226 AC: 34406 AN: 151998 Hom.: 4163 Cov.: 32 AF XY: 0.233 AC XY: 17281 AN XY: 74294

African (AFR) AF: 0.132 AC: 5470 AN: 41482

American (AMR) AF: 0.275 AC: 4200 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1412 AN: 5166

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4814

European-Finnish (FIN) AF: 0.300 AC: 3161 AN: 10546

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16323 AN: 67948

Other (OTH) AF: 0.271 AC: 571 AN: 2108

Alfa AF: 0.249 Hom.: 2617

Bravo AF: 0.216

Asia WGS AF: 0.331 AC: 1149 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.31
PhyloP100		0.44
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: rs7421482; hg19: chr2-115716385;