rs4624391

Variant names:

• chr2-115113689-A-C
• rs4624391
• NM_020868.6:c.61-195550A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-115113689-A-C
• chr2-115113689-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020868.6(DPP10):​c.61-195550A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,872 control chromosomes in the GnomAD database, including 18,037 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 0.48 (18037 hom., cov: 32)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 6 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]

LOC105373574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.61-195550A>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.61-195550A>C		intron_variant	Intron 1 of 25	1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72898 AN: 151754 Hom.: 18012 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.481 AC: 72986 AN: 151872 Hom.: 18037 Cov.: 32 AF XY: 0.482 AC XY: 35790 AN XY: 74218

African (AFR) AF: 0.565 AC: 23383 AN: 41386

American (AMR) AF: 0.509 AC: 7765 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3430 AN: 5142

South Asian (SAS) AF: 0.434 AC: 2087 AN: 4814

European-Finnish (FIN) AF: 0.458 AC: 4831 AN: 10558

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28163 AN: 67952

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.455 Hom.: 5239

Bravo AF: 0.493

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.75
PhyloP100		-1.8
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: rs4624391; hg19: chr2-115871266; COSMIC: COSV67714036;