2-115373461-T-C

Variant names:

• chr2-115373461-T-C
• rs11898241
• NM_020868.6:c.271+29549T>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.271+29549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,748 control chromosomes in the GnomAD database, including 35,223 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 0.68 (35223 hom., cov: 30)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.271+29549T>C		intron_variant	Intron 3 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.271+29549T>C		intron_variant	Intron 3 of 25	1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102857 AN: 151630 Hom.: 35207 Cov.: 30

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.678 AC: 102925 AN: 151748 Hom.: 35223 Cov.: 30 AF XY: 0.677 AC XY: 50234 AN XY: 74150

African (AFR) AF: 0.594 AC: 24555 AN: 41326

American (AMR) AF: 0.754 AC: 11516 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2044 AN: 3462

East Asian (EAS) AF: 0.699 AC: 3574 AN: 5112

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4814

European-Finnish (FIN) AF: 0.694 AC: 7306 AN: 10528

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.716 AC: 48657 AN: 67924

Other (OTH) AF: 0.667 AC: 1407 AN: 2110

Alfa AF: 0.646 Hom.: 3587

Bravo AF: 0.679

Asia WGS AF: 0.684 AC: 2375 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.28
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: rs11898241; hg19: chr2-116131037;