7-154052720-CT-C

Variant summary

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

The NM_130797.4(DPP6):c.-88del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.25 (4372 hom., cov: 6)
  • Exomes 𝑓: 0.40 (3673 hom.)
  • Failed GnomAD Quality Control
• Consequence: DPP6 NM_130797.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0930

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 7-154052720-CT-C is Benign according to our data. Variant chr7-154052720-CT-C is described in ClinVar as [Benign]. Clinvar id is 1259138.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP6	NM_130797.4	c.-88del		5_prime_UTR_variant	1/26	ENST00000377770.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP6	ENST00000377770.8	c.-88del		5_prime_UTR_variant	1/26	1	NM_130797.4
DPP6	ENST00000406326.5	c.-88del		5_prime_UTR_variant	1/6	1
DPP6	ENST00000404039.5	c.51+164999del		intron_variant		1
DPP6	ENST00000706130.1	c.60+303725del		intron_variant

Frequencies

GnomAD3 genomes AF: 0.246 AC: 34774 AN: 141356 Hom.: 4379 Cov.: 6

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.237

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.400 AC: 300267 AN: 750086 Hom.: 3673 Cov.: 0 AF XY: 0.398 AC XY: 146689 AN XY: 368268

Gnomad4 AFR exome AF: 0.433

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.339

Gnomad4 EAS exome AF: 0.429

Gnomad4 SAS exome AF: 0.388

Gnomad4 FIN exome AF: 0.316

Gnomad4 NFE exome AF: 0.404

Gnomad4 OTH exome AF: 0.393

GnomAD4 genome AF: 0.246 AC: 34759 AN: 141346 Hom.: 4372 Cov.: 6 AF XY: 0.247 AC XY: 16887 AN XY: 68326

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.234

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

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs571183490; hg19: chr7-153749805;