chr2-114453065-A-C

Variant names:

• chr2-114453065-A-C
• rs1430090
• NM_020868.6:c.60+10227A>C

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+10227A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,066 control chromosomes in the GnomAD database, including 5,980 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 0.26 (5980 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 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+10227A>C		intron	N/A	NP_065919.3
	DPP10	NM_001321907.3		c.60+10227A>C		intron	N/A	NP_001308836.2
	DPP10	NM_001321910.3		c.-149+10227A>C		intron	N/A	NP_001308839.2	Q8N608-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.60+10227A>C		intron	N/A	ENSP00000386565.1	Q8N608-1
	DPP10	ENST00000436732.5	TSL:4	c.-163+10227A>C		intron	N/A	ENSP00000391092.1	C9J4M8

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39969 AN: 151948 Hom.: 5978 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.263 AC: 39968 AN: 152066 Hom.: 5980 Cov.: 32 AF XY: 0.269 AC XY: 19963 AN XY: 74326

African (AFR) AF: 0.136 AC: 5635 AN: 41500

American (AMR) AF: 0.210 AC: 3215 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3468

East Asian (EAS) AF: 0.383 AC: 1978 AN: 5164

South Asian (SAS) AF: 0.308 AC: 1485 AN: 4824

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10556

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21701 AN: 67960

Other (OTH) AF: 0.250 AC: 529 AN: 2112

Alfa AF: 0.296 Hom.: 27253

Bravo AF: 0.241

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.58
PhyloP100		1.0
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: rs1430090; hg19: chr2-115210642;