rs980316

Variant names:

• chr2-114953249-T-C
• rs980316
• NM_020868.6:c.61-355990T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-114953249-T-C
• chr2-114953249-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.94).
• 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 rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.61-355990T>C		intron_variant	Intron 1 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.61-355990T>C		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1
DPP10	ENST00000409163.5	c.-90-355990T>C		intron_variant	Intron 2 of 26	2		ENSP00000387038.1
DPP10	ENST00000436732.5	c.-162-96899T>C		intron_variant	Intron 1 of 4	4		ENSP00000391092.1
DPP10	ENST00000461250.5	n.654+246075T>C		intron_variant	Intron 3 of 7	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

African (AFR) AF: 0.162 AC: 6738 AN: 41518

American (AMR) AF: 0.348 AC: 5307 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2039 AN: 5158

South Asian (SAS) AF: 0.437 AC: 2108 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4279 AN: 10542

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23415 AN: 67958

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.339 Hom.: 17271

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
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs980316; hg19: chr2-115710826; COSMIC: COSV107512783;