chr17-70169740-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000891.3(KCNJ2):c.-217+39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 153,612 control chromosomes in the GnomAD database, including 982 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.062 ( 978 hom., cov: 32)
Exomes 𝑓: 0.012 ( 4 hom. )
Consequence
KCNJ2
NM_000891.3 intron
NM_000891.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.146
Genes affected
KCNJ2 (HGNC:6263): (potassium inwardly rectifying channel subfamily J member 2) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein, which has a greater tendency to allow potassium to flow into a cell rather than out of a cell, probably participates in establishing action potential waveform and excitability of neuronal and muscle tissues. Mutations in this gene have been associated with Andersen syndrome, which is characterized by periodic paralysis, cardiac arrhythmias, and dysmorphic features. [provided by RefSeq, Jul 2008]
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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=-0.82).
BP6
?
Variant 17-70169740-C-T is Benign according to our data. Variant chr17-70169740-C-T is described in ClinVar as [Benign]. Clinvar id is 1229696.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ2 | NM_000891.3 | c.-217+39C>T | intron_variant | ENST00000243457.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ2 | ENST00000243457.4 | c.-217+39C>T | intron_variant | 1 | NM_000891.3 | P1 | |||
KCNJ2 | ENST00000535240.1 | c.-217+883C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0614 AC: 9344AN: 152074Hom.: 965 Cov.: 32
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GnomAD4 exome AF: 0.0120 AC: 17AN: 1420Hom.: 4 Cov.: 0 AF XY: 0.00642 AC XY: 7AN XY: 1090
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GnomAD4 genome ? AF: 0.0617 AC: 9387AN: 152192Hom.: 978 Cov.: 32 AF XY: 0.0599 AC XY: 4459AN XY: 74402
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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 03, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at