rs17764121

Positions:

• chr2-114471683-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_020868.6(DPP10):​c.60+28845T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 152,340 control chromosomes in the GnomAD database, including 58 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 0.023 (58 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

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=-0.86).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0233 (3551/152340) while in subpopulation SAS AF= 0.0496 (239/4820). AF 95% confidence interval is 0.0444. There are 58 homozygotes in gnomad4. There are 1695 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 58 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP10	NM_020868.6	c.60+28845T>C		intron_variant		ENST00000410059.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP10	ENST00000410059.6	c.60+28845T>C		intron_variant		1	NM_020868.6	A1
DPP10	ENST00000409163.5	c.-91+8257T>C		intron_variant		2
DPP10	ENST00000436732.5	c.-163+28845T>C		intron_variant		4
DPP10	ENST00000461250.5	n.596+8257T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0233 AC: 3554 AN: 152222 Hom.: 58 Cov.: 32

Gnomad AFR AF: 0.00531

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.0186

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0233 AC: 3551 AN: 152340 Hom.: 58 Cov.: 32 AF XY: 0.0228 AC XY: 1695 AN XY: 74498

Gnomad4 AFR AF: 0.00529

Gnomad4 AMR AF: 0.0185

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0496

Gnomad4 FIN AF: 0.0186

Gnomad4 NFE AF: 0.0345

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0258 Hom.: 11

Bravo AF: 0.0218

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17764121; hg19: chr2-115229260;