2-114930953-C-T

Position:

• chr2-114930953-C-T

Variant summary

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

The NM_020868.6(DPP10):​c.61-378286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,238 control chromosomes in the GnomAD database, including 1,318 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 0.12 (1318 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.61-378286C>T		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.61-378286C>T		intron_variant		1	NM_020868.6	A1
DPP10	ENST00000409163.5	c.-90-378286C>T		intron_variant		2
DPP10	ENST00000436732.5	c.-162-119195C>T		intron_variant		4
DPP10	ENST00000461250.5	n.654+223779C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18995 AN: 152120 Hom.: 1316 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.125 AC: 19011 AN: 152238 Hom.: 1318 Cov.: 33 AF XY: 0.124 AC XY: 9217 AN XY: 74426

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0441

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.127

Alfa AF: 0.135 Hom.: 2141

Bravo AF: 0.121

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1914973; hg19: chr2-115688530;