Variant 7-154052934-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_130797.4(DPP6):c.114C>T(p.Gly38Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,453,984 control chromosomes in the GnomAD database, including 16,059 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1172 hom., cov: 31)

Exomes 𝑓: 0.15 ( 14887 hom. )

Consequence

DPP6
NM_130797.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.345

Variant links:

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]

DPP6 links:

DPP6 (HGNC:):

DPP6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 7-154052934-C-T is Benign according to our data. Variant chr7-154052934-C-T is described in ClinVar as [Benign]. Clinvar id is 1247688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-154052934-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.345 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP6	NM_130797.4 linkuse as main transcript	c.114C>T	p.Gly38Gly	synonymous_variant	1/26	ENST00000377770.8	NP_570629.2	P42658-1Q8IYG9A7E2E4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DPP6	ENST00000377770.8 linkuse as main transcript	c.114C>T	p.Gly38Gly	synonymous_variant	1/26	1	NM_130797.4	ENSP00000367001.3	P42658-1
DPP6	ENST00000406326.5 linkuse as main transcript	c.114C>T	p.Gly38Gly	synonymous_variant	1/6	1		ENSP00000384393.1	Q8IYG9
DPP6	ENST00000404039.5 linkuse as main transcript	c.51+165200C>T		intron_variant		1		ENSP00000385578.1	E9PF59
DPP6	ENST00000706130.1 linkuse as main transcript	c.60+303926C>T		intron_variant				ENSP00000516215.1	A0A994J7K0

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17451

AN:

148304

Hom.:

1173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0543

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.00275

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.202

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.125

GnomAD3 exomes

AF:

0.131

AC:

14131

AN:

108040

Hom.:

1101

AF XY:

0.135

AC XY:

8112

AN XY:

59944

show subpopulations

Gnomad AFR exome

AF:

0.0683

Gnomad AMR exome

AF:

0.0697

Gnomad ASJ exome

AF:

0.138

Gnomad EAS exome

AF:

0.00563

Gnomad SAS exome

AF:

0.164

Gnomad FIN exome

AF:

0.136

Gnomad NFE exome

AF:

0.165

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.148

AC:

193698

AN:

1305578

Hom.:

14887

Cov.:

AF XY:

0.149

AC XY:

96273

AN XY:

644242

show subpopulations

Gnomad4 AFR exome

AF:

0.0492

Gnomad4 AMR exome

AF:

0.0721

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.00323

Gnomad4 SAS exome

AF:

0.161

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.158

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.118

AC:

17448

AN:

148406

Hom.:

1172

Cov.:

AF XY:

0.116

AC XY:

8427

AN XY:

72376

show subpopulations

Gnomad4 AFR

AF:

0.0542

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.00276

Gnomad4 SAS

AF:

0.153

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.123

Alfa

AF:

0.137

Hom.:

328

Bravo

AF:

0.110

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.96

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over