7-154669402-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_130797.4(DPP6):āc.723A>Gā(p.Lys241=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 1,556,854 control chromosomes in the GnomAD database, including 615,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.83 ( 52939 hom., cov: 33)
Exomes š: 0.89 ( 562280 hom. )
Consequence
DPP6
NM_130797.4 synonymous
NM_130797.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.500
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 Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 7-154669402-A-G is Benign according to our data. Variant chr7-154669402-A-G is described in ClinVar as [Benign]. Clinvar id is 1174770.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-154669402-A-G is described in Lovd as [Likely_benign]. Variant chr7-154669402-A-G is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.5 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP6 | NM_130797.4 | c.723A>G | p.Lys241= | synonymous_variant | 7/26 | ENST00000377770.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000377770.8 | c.723A>G | p.Lys241= | synonymous_variant | 7/26 | 1 | NM_130797.4 |
Frequencies
GnomAD3 genomes AF: 0.828 AC: 125976AN: 152086Hom.: 52918 Cov.: 33
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GnomAD3 exomes AF: 0.869 AC: 145053AN: 166836Hom.: 63394 AF XY: 0.875 AC XY: 76902AN XY: 87918
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GnomAD4 exome AF: 0.894 AC: 1255315AN: 1404650Hom.: 562280 Cov.: 67 AF XY: 0.893 AC XY: 619288AN XY: 693224
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GnomAD4 genome AF: 0.828 AC: 126041AN: 152204Hom.: 52939 Cov.: 33 AF XY: 0.828 AC XY: 61647AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
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 | - | - - |
Ventricular fibrillation, paroxysmal familial, 2;C4225375:Intellectual disability, autosomal dominant 33 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 11, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at