rs201012161
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_172107.4(KCNQ2):c.816+10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000044 ( 0 hom. )
Consequence
KCNQ2
NM_172107.4 intron
NM_172107.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.198
Genes affected
KCNQ2 (HGNC:6296): (potassium voltage-gated channel subfamily Q member 2) The M channel is a slowly activating and deactivating potassium channel that plays a critical role in the regulation of neuronal excitability. The M channel is formed by the association of the protein encoded by this gene and a related protein encoded by the KCNQ3 gene, both integral membrane proteins. M channel currents are inhibited by M1 muscarinic acetylcholine receptors and activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 1 (BFNC), also known as epilepsy, benign neonatal type 1 (EBN1). At least five transcript variants encoding five different isoforms 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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 20-63442396-C-A is Benign according to our data. Variant chr20-63442396-C-A is described in ClinVar as [Benign]. Clinvar id is 530560.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ2 | NM_172107.4 | c.816+10G>T | intron_variant | ENST00000359125.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ2 | ENST00000359125.7 | c.816+10G>T | intron_variant | 1 | NM_172107.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152020Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251370Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135862
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GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 727154
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GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152020Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74238
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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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