chr2-115132527-T-C

Variant names:

• chr2-115132527-T-C
• rs4491738
• NM_020868.6:c.61-176712T>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.61-176712T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,168 control chromosomes in the GnomAD database, including 1,354 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 0.11 (1354 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• 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]

DPP10-AS1 (HGNC:40941): (DPP10 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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.61-176712T>C		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.112-176712T>C		intron	N/A	NP_001308834.2
	DPP10	NM_001178037.3		c.48+67722T>C		intron	N/A	NP_001171508.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.61-176712T>C		intron	N/A	ENSP00000386565.1	Q8N608-1
	DPP10	ENST00000409163.5	TSL:2	c.-90-176712T>C		intron	N/A	ENSP00000387038.1	Q8N608-4
	DPP10	ENST00000393146.6	TSL:5	c.48+67722T>C		intron	N/A	ENSP00000376854.2	J3KPP1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17407 AN: 152050 Hom.: 1343 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.115 AC: 17459 AN: 152168 Hom.: 1354 Cov.: 31 AF XY: 0.118 AC XY: 8792 AN XY: 74414

African (AFR) AF: 0.156 AC: 6460 AN: 41500

American (AMR) AF: 0.196 AC: 2991 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1542 AN: 5160

South Asian (SAS) AF: 0.161 AC: 778 AN: 4820

European-Finnish (FIN) AF: 0.0598 AC: 634 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0679 AC: 4617 AN: 68022

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.0860 Hom.: 3387

Bravo AF: 0.129

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.85
DANN	Benign	0.49
PhyloP100		-1.7
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: rs4491738; hg19: chr2-115890104;