2-115474205-A-G

Variant names:

• chr2-115474205-A-G
• rs11123306
• NM_020868.6:c.272-25305A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.272-25305A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,052 control chromosomes in the GnomAD database, including 24,523 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 0.55 (24523 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.272-25305A>G		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.272-25305A>G		intron_variant	Intron 3 of 25	1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83634 AN: 151934 Hom.: 24513 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.550 AC: 83673 AN: 152052 Hom.: 24523 Cov.: 33 AF XY: 0.544 AC XY: 40435 AN XY: 74316

African (AFR) AF: 0.372 AC: 15434 AN: 41494

American (AMR) AF: 0.516 AC: 7883 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2342 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1789 AN: 5142

South Asian (SAS) AF: 0.532 AC: 2564 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5865 AN: 10564

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

European-Non Finnish (NFE) AF: 0.675 AC: 45858 AN: 67980

Other (OTH) AF: 0.572 AC: 1206 AN: 2110

Alfa AF: 0.581 Hom.: 4651

Bravo AF: 0.536

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.75
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11123306; hg19: chr2-116231781;