rs17764121

Variant names:

• chr2-114471683-T-C
• rs17764121
• NM_020868.6:c.60+28845T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 58 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020868.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	NM_020868.6	MANE Select	c.60+28845T>C		intron	N/A	NP_065919.3
	DPP10	NM_001321905.3		c.53+9543T>C		intron	N/A	NP_001308834.2
	DPP10	NM_001321907.3		c.60+28845T>C		intron	N/A	NP_001308836.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP10	ENST00000410059.6	TSL:1 MANE Select	c.60+28845T>C		intron	N/A	ENSP00000386565.1
	DPP10	ENST00000409163.5	TSL:2	c.-91+8257T>C		intron	N/A	ENSP00000387038.1
	DPP10	ENST00000436732.5	TSL:4	c.-163+28845T>C		intron	N/A	ENSP00000391092.1

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

African (AFR) AF: 0.00529 AC: 220 AN: 41584

American (AMR) AF: 0.0185 AC: 283 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0496 AC: 239 AN: 4820

European-Finnish (FIN) AF: 0.0186 AC: 198 AN: 10622

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0345 AC: 2344 AN: 68032

Other (OTH) AF: 0.0194 AC: 41 AN: 2116

Alfa AF: 0.0247 Hom.: 44

Bravo AF: 0.0218

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17764121; hg19: chr2-115229260;