rs1611001

chr7-154612851-ATTGGGCTTATT-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_130797.4(DPP6):c.628-24969_628-24959del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (13439 hom., cov: 0)
• Consequence: DPP6 NM_130797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

DPP6 (HGNC:3010): (dipeptidyl peptidase like 6) This gene encodes a single-pass type II membrane protein that is a member of the peptidase S9B family of 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. Variations in this gene may be associated with susceptibility to amyotrophic lateral sclerosis and with idiopathic ventricular fibrillation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP6	NM_130797.4	c.628-24969_628-24959del		intron_variant		ENST00000377770.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP6	ENST00000377770.8	c.628-24969_628-24959del		intron_variant		1	NM_130797.4

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61437 AN: 151954 Hom.: 13428 Cov.: 0

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.404 AC: 61475 AN: 152072 Hom.: 13439 Cov.: 0 AF XY: 0.411 AC XY: 30557 AN XY: 74322

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.446

Alfa AF: 0.406 Hom.: 1409

Asia WGS AF: 0.582 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611001; hg19: chr7-154404561; COSMIC: COSV59650498;