chr2-26692756-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_002246.3(KCNK3):c.-120G>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 0.574 in 465,024 control chromosomes in the GnomAD database, including 80,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.50 ( 20193 hom., cov: 30)
Exomes 𝑓: 0.61 ( 60667 hom. )
Consequence
KCNK3
NM_002246.3 5_prime_UTR
NM_002246.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.398
Genes affected
KCNK3 (HGNC:6278): (potassium two pore domain channel subfamily K member 3) This gene encodes a member of the superfamily of potassium channel proteins that contain two pore-forming P domains. The encoded protein is an outwardly rectifying channel that is sensitive to changes in extracellular pH and is inhibited by extracellular acidification. Also referred to as an acid-sensitive potassium channel, it is activated by the anesthetics halothane and isoflurane. Although three transcripts are detected in northern blots, there is currently no sequence available to confirm transcript variants for this gene. [provided by RefSeq, Aug 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=-0.35).
BP6
?
Variant 2-26692756-G-T is Benign according to our data. Variant chr2-26692756-G-T is described in ClinVar as [Benign]. Clinvar id is 1235279.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNK3 | NM_002246.3 | c.-120G>T | 5_prime_UTR_variant | 1/2 | ENST00000302909.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK3 | ENST00000302909.4 | c.-120G>T | 5_prime_UTR_variant | 1/2 | 1 | NM_002246.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.496 AC: 72505AN: 146186Hom.: 20180 Cov.: 30
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GnomAD4 exome AF: 0.610 AC: 194573AN: 318728Hom.: 60667 Cov.: 5 AF XY: 0.610 AC XY: 92685AN XY: 151824
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GnomAD4 genome ? AF: 0.496 AC: 72550AN: 146296Hom.: 20193 Cov.: 30 AF XY: 0.493 AC XY: 35118AN XY: 71180
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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 | Aug 25, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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