chr2-26728037-G-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002246.3(KCNK3):c.654G>T(p.Pro218=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00292 in 1,614,172 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 78 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 54 hom. )
Consequence
KCNK3
NM_002246.3 synonymous
NM_002246.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.41
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 2-26728037-G-T is Benign according to our data. Variant chr2-26728037-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 474322.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.41 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0532 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNK3 | NM_002246.3 | c.654G>T | p.Pro218= | synonymous_variant | 2/2 | ENST00000302909.4 | |
KCNK3 | XM_005264293.3 | c.324G>T | p.Pro108= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK3 | ENST00000302909.4 | c.654G>T | p.Pro218= | synonymous_variant | 2/2 | 1 | NM_002246.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0158 AC: 2408AN: 152230Hom.: 78 Cov.: 33
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GnomAD3 exomes AF: 0.00407 AC: 1022AN: 250872Hom.: 29 AF XY: 0.00293 AC XY: 398AN XY: 135678
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GnomAD4 exome AF: 0.00157 AC: 2299AN: 1461824Hom.: 54 Cov.: 31 AF XY: 0.00135 AC XY: 985AN XY: 727218
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GnomAD4 genome AF: 0.0158 AC: 2411AN: 152348Hom.: 78 Cov.: 33 AF XY: 0.0159 AC XY: 1186AN XY: 74496
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pulmonary hypertension, primary, 4 Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 23, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 21, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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