rs7779540
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000404039.5(DPP6):c.51+37843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 151,920 control chromosomes in the GnomAD database, including 350 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.066 ( 350 hom., cov: 31)
Consequence
DPP6
ENST00000404039.5 intron
ENST00000404039.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.81
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0827 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP6 | NM_001039350.3 | c.51+37843G>A | intron_variant | ||||
DPP6 | NM_001364497.2 | c.60+176569G>A | intron_variant | ||||
DPP6 | NM_001364498.2 | c.60+176569G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000404039.5 | c.51+37843G>A | intron_variant | 1 | |||||
DPP6 | ENST00000706130.1 | c.60+176569G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0657 AC: 9975AN: 151798Hom.: 350 Cov.: 31
GnomAD3 genomes
?
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0657 AC: 9981AN: 151920Hom.: 350 Cov.: 31 AF XY: 0.0633 AC XY: 4701AN XY: 74218
GnomAD4 genome
?
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9981
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151920
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31
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4701
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153
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at