7-154052113-GGGGC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000404039.5(DPP6):c.51+164380_51+164383del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.50 (18997 hom., cov: 0)
• Consequence: DPP6 ENST00000404039.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.163

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 -10 ACMG points.

• BP6: Variant 7-154052113-GGGGC-G is Benign according to our data. Variant chr7-154052113-GGGGC-G is described in ClinVar as [Benign]. Clinvar id is 1278530.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP6	NM_001039350.3	c.51+164380_51+164383del		intron_variant
DPP6	NM_001364497.2	c.60+303106_60+303109del		intron_variant
DPP6	NM_001364498.2	c.60+303106_60+303109del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP6	ENST00000404039.5	c.51+164380_51+164383del		intron_variant		1
DPP6	ENST00000706130.1	c.60+303106_60+303109del		intron_variant

Frequencies

GnomAD3 genomes AF: 0.497 AC: 73545 AN: 148058 Hom.: 18996 Cov.: 0

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.497 AC: 73566 AN: 148164 Hom.: 18997 Cov.: 0 AF XY: 0.501 AC XY: 36227 AN XY: 72318

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.491

Alfa AF: 0.507 Hom.: 2176

Bravo AF: 0.482

Asia WGS AF: 0.560 AC: 1925 AN: 3434

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

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: rs367576790; hg19: chr7-153749198;