chr22-38427131-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_152868.3(KCNJ4):c.1002A>G(p.Ser334=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 1,612,554 control chromosomes in the GnomAD database, including 350,395 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.70 ( 38630 hom., cov: 30)
Exomes 𝑓: 0.65 ( 311765 hom. )
Consequence
KCNJ4
NM_152868.3 synonymous
NM_152868.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.66
Genes affected
KCNJ4 (HGNC:6265): (potassium inwardly rectifying channel subfamily J member 4) Several different potassium channels are known to be involved with electrical signaling in the nervous system. One class is activated by depolarization whereas a second class is not. The latter are referred to as inwardly rectifying K+ channels, and they have a greater tendency to allow potassium to flow into the cell rather than out of it. This asymmetry in potassium ion conductance plays a key role in the excitability of muscle cells and neurons. The protein encoded by this gene is an integral membrane protein and member of the inward rectifier potassium channel family. The encoded protein has a small unitary conductance compared to other members of this protein family. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 22-38427131-T-C is Benign according to our data. Variant chr22-38427131-T-C is described in ClinVar as [Benign]. Clinvar id is 1274320.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-5.66 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ4 | NM_152868.3 | c.1002A>G | p.Ser334= | synonymous_variant | 2/2 | ENST00000303592.3 | |
LOC101927183 | XR_938252.3 | n.306+2159T>C | intron_variant, non_coding_transcript_variant | ||||
KCNJ4 | NM_004981.2 | c.1002A>G | p.Ser334= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ4 | ENST00000303592.3 | c.1002A>G | p.Ser334= | synonymous_variant | 2/2 | 1 | NM_152868.3 | P1 | |
ENST00000433230.1 | n.351T>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.704 AC: 106867AN: 151848Hom.: 38574 Cov.: 30
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GnomAD3 exomes AF: 0.697 AC: 173615AN: 249012Hom.: 62264 AF XY: 0.700 AC XY: 94617AN XY: 135120
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GnomAD4 exome AF: 0.647 AC: 945651AN: 1460588Hom.: 311765 Cov.: 65 AF XY: 0.653 AC XY: 474581AN XY: 726596
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GnomAD4 genome ? AF: 0.704 AC: 106979AN: 151966Hom.: 38630 Cov.: 30 AF XY: 0.710 AC XY: 52722AN XY: 74266
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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 | Apr 16, 2019 | - - |
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