chr2-114953249-T-C

Position:

• chr2-114953249-T-C

Variant summary

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

The NM_020868.6(DPP10):​c.61-355990T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,052 control chromosomes in the GnomAD database, including 7,825 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 0.31 (7825 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP10	NM_020868.6	c.61-355990T>C		intron_variant		ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.61-355990T>C		intron_variant		1	NM_020868.6	ENSP00000386565	A1
DPP10	ENST00000409163.5	c.-90-355990T>C		intron_variant		2		ENSP00000387038
DPP10	ENST00000436732.5	c.-162-96899T>C		intron_variant		4		ENSP00000391092
DPP10	ENST00000461250.5	n.654+246075T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46391 AN: 151934 Hom.: 7821 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.305 AC: 46419 AN: 152052 Hom.: 7825 Cov.: 32 AF XY: 0.313 AC XY: 23234 AN XY: 74334

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.357

Alfa AF: 0.344 Hom.: 13052

Bravo AF: 0.292

Asia WGS AF: 0.418 AC: 1452 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs980316; hg19: chr2-115710826;