2-115329056-A-T

Variant names:

• chr2-115329056-A-T
• rs925848
• NM_020868.6:c.176-14761A>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.176-14761A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,894 control chromosomes in the GnomAD database, including 37,338 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 0.70 (37338 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.753 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.176-14761A>T		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.227-14761A>T		intron	N/A	NP_001308834.2
	DPP10	NM_001178034.1		c.188-14761A>T		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.176-14761A>T		intron	N/A	ENSP00000386565.1	Q8N608-1
	DPP10	ENST00000393147.6	TSL:1	c.188-14761A>T		intron	N/A	ENSP00000376855.2	Q8N608-3
	DPP10	ENST00000310323.12	TSL:1	c.155-14761A>T		intron	N/A	ENSP00000309066.8	Q8N608-2

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105672 AN: 151778 Hom.: 37311 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.696 AC: 105751 AN: 151894 Hom.: 37338 Cov.: 32 AF XY: 0.696 AC XY: 51647 AN XY: 74236

African (AFR) AF: 0.572 AC: 23707 AN: 41416

American (AMR) AF: 0.765 AC: 11632 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3705 AN: 5138

South Asian (SAS) AF: 0.722 AC: 3482 AN: 4822

European-Finnish (FIN) AF: 0.753 AC: 7971 AN: 10584

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50975 AN: 67942

Other (OTH) AF: 0.687 AC: 1448 AN: 2108

Alfa AF: 0.719 Hom.: 4938

Bravo AF: 0.690

Asia WGS AF: 0.743 AC: 2582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		-0.080
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: rs925848; hg19: chr2-116086632;