chr7-154052668-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_130797.4(DPP6):c.-153C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 1,219,902 control chromosomes in the GnomAD database, including 200,802 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.54 ( 21948 hom., cov: 29)
Exomes 𝑓: 0.58 ( 178854 hom. )
Consequence
DPP6
NM_130797.4 5_prime_UTR
NM_130797.4 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.508
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 7-154052668-C-T is Benign according to our data. Variant chr7-154052668-C-T is described in ClinVar as [Benign]. Clinvar id is 1183923.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP6 | NM_130797.4 | c.-153C>T | 5_prime_UTR_variant | 1/26 | ENST00000377770.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000377770.8 | c.-153C>T | 5_prime_UTR_variant | 1/26 | 1 | NM_130797.4 | |||
DPP6 | ENST00000406326.5 | c.-153C>T | 5_prime_UTR_variant | 1/6 | 1 | ||||
DPP6 | ENST00000404039.5 | c.51+164934C>T | intron_variant | 1 | |||||
DPP6 | ENST00000706130.1 | c.60+303660C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.536 AC: 80355AN: 149894Hom.: 21933 Cov.: 29
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GnomAD4 exome AF: 0.575 AC: 615211AN: 1069926Hom.: 178854 Cov.: 32 AF XY: 0.577 AC XY: 298030AN XY: 516330
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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 | May 11, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at