rs379643
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138317.3(KCNK10):c.*2125T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,320 control chromosomes in the GnomAD database, including 7,985 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 0.31 ( 7977 hom., cov: 33)
Exomes 𝑓: 0.36 ( 8 hom. )
Consequence
KCNK10
NM_138317.3 3_prime_UTR
NM_138317.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.90
Genes affected
KCNK10 (HGNC:6273): (potassium two pore domain channel subfamily K member 10) The protein encoded by this gene belongs to the family of potassium channel proteins containing two pore-forming P domains. This channel is an open rectifier which primarily passes outward current under physiological K+ concentrations, and is stimulated strongly by arachidonic acid and to a lesser degree by membrane stretching, intracellular acidification, and general anaesthetics. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Sep 2008]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNK10 | NM_138317.3 | c.*2125T>C | 3_prime_UTR_variant | 7/7 | ENST00000319231.10 | ||
KCNK10 | NM_021161.5 | c.*2125T>C | 3_prime_UTR_variant | 7/7 | |||
KCNK10 | NM_138318.3 | c.*2125T>C | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK10 | ENST00000319231.10 | c.*2125T>C | 3_prime_UTR_variant | 7/7 | 1 | NM_138317.3 | P1 | ||
KCNK10 | ENST00000340700.9 | c.*2125T>C | 3_prime_UTR_variant | 7/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.314 AC: 47805AN: 152070Hom.: 7969 Cov.: 33
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33
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GnomAD4 exome AF: 0.356 AC: 47AN: 132Hom.: 8 Cov.: 0 AF XY: 0.361 AC XY: 26AN XY: 72
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GnomAD4 genome ? AF: 0.314 AC: 47833AN: 152188Hom.: 7977 Cov.: 33 AF XY: 0.311 AC XY: 23159AN XY: 74418
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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