Variant 7-154052919-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_130797.4(DPP6):c.99C>G(p.Pro33Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000447 in 1,496,680 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00045 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00045 ( 1 hom. )

Consequence

DPP6
NM_130797.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.19

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 7-154052919-C-G is Benign according to our data. Variant chr7-154052919-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2658247.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.19 with no splicing effect.

BS2

High AC in GnomAd4 at 68 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP6	NM_130797.4 linkuse as main transcript	c.99C>G	p.Pro33Pro	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.99C>G	p.Pro33Pro	synonymous_variant	1/26	1	NM_130797.4	ENSP00000367001.3	P42658-1
DPP6	ENST00000406326.5 linkuse as main transcript	c.99C>G	p.Pro33Pro	synonymous_variant	1/6	1		ENSP00000384393.1	Q8IYG9
DPP6	ENST00000404039.5 linkuse as main transcript	c.51+165185C>G		intron_variant		1		ENSP00000385578.1	E9PF59
DPP6	ENST00000706130.1 linkuse as main transcript	c.60+303911C>G		intron_variant				ENSP00000516215.1	A0A994J7K0

Frequencies

GnomAD3 genomes

AF:

0.000454

AC:

AN:

149632

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000243

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000267

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000419

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000743

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000446

AC:

AN:

123186

Hom.:

AF XY:

0.000488

AC XY:

AN XY:

67588

show subpopulations

Gnomad AFR exome

AF:

0.000232

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000923

Gnomad FIN exome

AF:

0.000389

Gnomad NFE exome

AF:

0.000913

Gnomad OTH exome

AF:

0.000545

GnomAD4 exome

AF:

0.000446

AC:

601

AN:

1346944

Hom.:

Cov.:

AF XY:

0.000463

AC XY:

308

AN XY:

664774

show subpopulations

Gnomad4 AFR exome

AF:

0.0000346

Gnomad4 AMR exome

AF:

0.000265

Gnomad4 ASJ exome

AF:

0.0000423

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000256

Gnomad4 FIN exome

AF:

0.000340

Gnomad4 NFE exome

AF:

0.000522

Gnomad4 OTH exome

AF:

0.000434

GnomAD4 genome

AF:

0.000454

AC:

AN:

149736

Hom.:

Cov.:

AF XY:

0.000328

AC XY:

AN XY:

73120

show subpopulations

Gnomad4 AFR

AF:

0.000243

Gnomad4 AMR

AF:

0.000266

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000419

Gnomad4 NFE

AF:

0.000743

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000467

Hom.:

Bravo

AF:

0.000544

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

DPP6: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.71

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