rs6732028

Positions:

• chr2-114829362-A-G

Variant summary

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

The NM_020868.6(DPP10):​c.60+386524A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 149,898 control chromosomes in the GnomAD database, including 12,347 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 0.40 (12347 hom., cov: 27)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

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]

DPP10-AS3 (HGNC:40939): (DPP10 antisense RNA 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.60+386524A>G		intron_variant		ENST00000410059.6	NP_065919.3
DPP10-AS3	NR_132105.1	n.225-490T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.60+386524A>G		intron_variant		1	NM_020868.6	ENSP00000386565	A1
DPP10-AS3	ENST00000417844.1	n.225-490T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 59747 AN: 149806 Hom.: 12342 Cov.: 27

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.399 AC: 59766 AN: 149898 Hom.: 12347 Cov.: 27 AF XY: 0.395 AC XY: 28831 AN XY: 72974

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.413

Alfa AF: 0.442 Hom.: 19333

Bravo AF: 0.381

Asia WGS AF: 0.270 AC: 938 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6732028; hg19: chr2-115586939; COSMIC: COSV68840769; COSMIC: COSV68840769;