7-154052113-GGGGC-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001364497.2(DPP6):c.60+303106_60+303109delGGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.50 ( 18997 hom., cov: 0)
Consequence
DPP6
NM_001364497.2 intron
NM_001364497.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.163
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 -10 ACMG points.
BP6
Variant 7-154052113-GGGGC-G is Benign according to our data. Variant chr7-154052113-GGGGC-G is described in ClinVar as [Benign]. Clinvar id is 1278530.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPP6 | NM_001364497.2 | c.60+303106_60+303109delGGGC | intron_variant | NP_001351426.1 | ||||
DPP6 | NM_001364498.2 | c.60+303106_60+303109delGGGC | intron_variant | NP_001351427.1 | ||||
DPP6 | NM_001364499.2 | c.60+303106_60+303109delGGGC | intron_variant | NP_001351428.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000404039.5 | c.51+164380_51+164383delGGGC | intron_variant | 1 | ENSP00000385578.1 | |||||
DPP6 | ENST00000706130.1 | c.60+303106_60+303109delGGGC | intron_variant | ENSP00000516215.1 |
Frequencies
GnomAD3 genomes AF: 0.497 AC: 73545AN: 148058Hom.: 18996 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.497 AC: 73566AN: 148164Hom.: 18997 Cov.: 0 AF XY: 0.501 AC XY: 36227AN XY: 72318
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at