rs7576583

Positions:

• chr2-115582237-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.441+56265T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,470 control chromosomes in the GnomAD database, including 2,839 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 0.15 (2839 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.441+56265T>G		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.441+56265T>G		intron_variant		1	NM_020868.6	A1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23059 AN: 151352 Hom.: 2833 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.153 AC: 23101 AN: 151470 Hom.: 2839 Cov.: 32 AF XY: 0.151 AC XY: 11194 AN XY: 73954

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.0864

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.139

Alfa AF: 0.122 Hom.: 219

Bravo AF: 0.160

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.22

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

Publications

LitVar

Other links and lift over

dbSNP: rs7576583; hg19: chr2-116339813;