2-114514264-C-T

Variant names:

• chr2-114514264-C-T
• rs10187644
• NM_020868.6:c.60+71426C>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.60+71426C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,862 control chromosomes in the GnomAD database, including 13,992 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 0.43 (13992 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 3 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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.443 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.60+71426C>T		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.53+52124C>T		intron	N/A	NP_001308834.2
	DPP10	NM_001321907.3		c.60+71426C>T		intron	N/A	NP_001308836.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.60+71426C>T		intron	N/A	ENSP00000386565.1	Q8N608-1
	DPP10	ENST00000409163.5	TSL:2	c.-91+50838C>T		intron	N/A	ENSP00000387038.1	Q8N608-4
	DPP10	ENST00000436732.5	TSL:4	c.-163+71426C>T		intron	N/A	ENSP00000391092.1	C9J4M8

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64954 AN: 151744 Hom.: 13979 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.428 AC: 64984 AN: 151862 Hom.: 13992 Cov.: 32 AF XY: 0.434 AC XY: 32233 AN XY: 74198

African (AFR) AF: 0.437 AC: 18065 AN: 41380

American (AMR) AF: 0.358 AC: 5471 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2350 AN: 5168

South Asian (SAS) AF: 0.459 AC: 2198 AN: 4792

European-Finnish (FIN) AF: 0.557 AC: 5870 AN: 10530

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28440 AN: 67932

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.407 Hom.: 21983

Bravo AF: 0.412

Asia WGS AF: 0.443 AC: 1540 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	3.3
DANN	Benign	0.25
PhyloP100		0.027
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: rs10187644; hg19: chr2-115271841; COSMIC: COSV69325961;