chr2-114636950-C-T

Position:

• chr2-114636950-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.60+194112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,762 control chromosomes in the GnomAD database, including 2,319 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 0.16 (2319 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553

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 (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.60+194112C>T		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.60+194112C>T		intron_variant		1	NM_020868.6	A1
DPP10	ENST00000409163.5	c.-91+173524C>T		intron_variant		2
DPP10	ENST00000436732.5	c.-163+194112C>T		intron_variant		4
DPP10	ENST00000461250.5	n.597-70167C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23958 AN: 151642 Hom.: 2318 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.158 AC: 23998 AN: 151762 Hom.: 2319 Cov.: 32 AF XY: 0.156 AC XY: 11602 AN XY: 74194

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.153

Alfa AF: 0.133 Hom.: 1535

Bravo AF: 0.164

Asia WGS AF: 0.135 AC: 472 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	8.6
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: rs12996109; hg19: chr2-115394527;