2-115672214-T-C

Variant names:

• chr2-115672214-T-C
• rs4075701
• NM_020868.6:c.442-17473T>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.442-17473T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,956 control chromosomes in the GnomAD database, including 37,904 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 (37904 hom., cov: 31)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.442-17473T>C		intron_variant	Intron 5 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.442-17473T>C		intron_variant	Intron 5 of 25	1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103930 AN: 151840 Hom.: 37898 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.684 AC: 103964 AN: 151956 Hom.: 37904 Cov.: 31 AF XY: 0.688 AC XY: 51092 AN XY: 74268

African (AFR) AF: 0.409 AC: 16944 AN: 41416

American (AMR) AF: 0.782 AC: 11942 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4722 AN: 5156

South Asian (SAS) AF: 0.707 AC: 3403 AN: 4812

European-Finnish (FIN) AF: 0.799 AC: 8439 AN: 10564

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53434 AN: 67952

Other (OTH) AF: 0.693 AC: 1463 AN: 2110

Alfa AF: 0.758 Hom.: 22403

Bravo AF: 0.676

Asia WGS AF: 0.735 AC: 2552 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		-0.049
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: rs4075701; hg19: chr2-116429790;