chr2-115546355-C-G

Variant names:

• chr2-115546355-C-G
• rs6741692
• NM_020868.6:c.441+20383C>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.441+20383C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,986 control chromosomes in the GnomAD database, including 25,755 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 0.56 (25755 hom., cov: 33)
• Consequence: DPP10 NM_020868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPP10	NM_020868.6	c.441+20383C>G		intron_variant	Intron 5 of 25	ENST00000410059.6	NP_065919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPP10	ENST00000410059.6	c.441+20383C>G		intron_variant	Intron 5 of 25	1	NM_020868.6	ENSP00000386565.1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85589 AN: 151868 Hom.: 25745 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.563 AC: 85632 AN: 151986 Hom.: 25755 Cov.: 33 AF XY: 0.558 AC XY: 41475 AN XY: 74274

African (AFR) AF: 0.375 AC: 15562 AN: 41474

American (AMR) AF: 0.524 AC: 7985 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2393 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1790 AN: 5138

South Asian (SAS) AF: 0.535 AC: 2582 AN: 4828

European-Finnish (FIN) AF: 0.611 AC: 6456 AN: 10558

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46913 AN: 67954

Other (OTH) AF: 0.581 AC: 1225 AN: 2110

Alfa AF: 0.507 Hom.: 1571

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0090
DANN	Benign	0.27
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6741692; hg19: chr2-116303931;