2-115313789-C-T

Variant names:

• chr2-115313789-C-T
• rs6542256
• NM_020868.6:c.175+4436C>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.175+4436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,260 control chromosomes in the GnomAD database, including 61,960 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 0.90 (61960 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 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.175+4436C>T		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.226+4436C>T		intron	N/A	NP_001308834.2
	DPP10	NM_001178034.1		c.187+4436C>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.175+4436C>T		intron	N/A	ENSP00000386565.1	Q8N608-1
	DPP10	ENST00000393147.6	TSL:1	c.187+4436C>T		intron	N/A	ENSP00000376855.2	Q8N608-3
	DPP10	ENST00000310323.12	TSL:1	c.154+4436C>T		intron	N/A	ENSP00000309066.8	Q8N608-2

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137098 AN: 152142 Hom.: 61908 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.901 AC: 137211 AN: 152260 Hom.: 61960 Cov.: 33 AF XY: 0.899 AC XY: 66931 AN XY: 74434

African (AFR) AF: 0.945 AC: 39279 AN: 41556

American (AMR) AF: 0.878 AC: 13412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3839 AN: 5174

South Asian (SAS) AF: 0.815 AC: 3938 AN: 4830

European-Finnish (FIN) AF: 0.928 AC: 9841 AN: 10608

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 61016 AN: 68024

Other (OTH) AF: 0.877 AC: 1848 AN: 2106

Alfa AF: 0.901 Hom.: 60244

Bravo AF: 0.898

Asia WGS AF: 0.815 AC: 2828 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.19
PhyloP100		-0.099
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: rs6542256; hg19: chr2-116071365;