chr7-154052986-CGCG-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_130797.4(DPP6):c.185_187del(p.Gly62del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 146,920 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000061 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00043 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DPP6
NM_130797.4 inframe_deletion
NM_130797.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.431
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
?
Variant 7-154052986-CGCG-C is Benign according to our data. Variant chr7-154052986-CGCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 1299926.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr7-154052986-CGCG-C is described in Lovd as [Likely_benign].
BS2
?
High AC in GnomAd at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP6 | NM_130797.4 | c.185_187del | p.Gly62del | inframe_deletion | 1/26 | ENST00000377770.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000377770.8 | c.185_187del | p.Gly62del | inframe_deletion | 1/26 | 1 | NM_130797.4 | ||
DPP6 | ENST00000406326.5 | c.185_187del | p.Gly62del | inframe_deletion | 1/6 | 1 | |||
DPP6 | ENST00000404039.5 | c.51+165271_51+165273del | intron_variant | 1 | |||||
DPP6 | ENST00000706130.1 | c.60+303997_60+303999del | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000613 AC: 9AN: 146824Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00162 AC: 5AN: 3080Hom.: 0 AF XY: 0.00177 AC XY: 3AN XY: 1692
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000428 AC: 394AN: 921448Hom.: 0 AF XY: 0.000498 AC XY: 215AN XY: 431814
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GnomAD4 genome ? AF: 0.0000613 AC: 9AN: 146920Hom.: 0 Cov.: 31 AF XY: 0.0000419 AC XY: 3AN XY: 71542
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at