rs886049507
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000217.3(KCNA1):c.-230C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000225 in 445,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000022 ( 0 hom. )
Consequence
KCNA1
NM_000217.3 5_prime_UTR
NM_000217.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.89
Publications
0 publications found
Genes affected
KCNA1 (HGNC:6218): (potassium voltage-gated channel subfamily A member 1) This gene encodes a voltage-gated delayed potassium channel that is phylogenetically related to the Drosophila Shaker channel. The encoded protein has six putative transmembrane segments (S1-S6), and the loop between S5 and S6 forms the pore and contains the conserved selectivity filter motif (GYGD). The functional channel is a homotetramer. The N-terminus of the channel is associated with beta subunits that can modify the inactivation properties of the channel as well as affect expression levels. The C-terminus of the channel is complexed to a PDZ domain protein that is responsible for channel targeting. Mutations in this gene have been associated with myokymia with periodic ataxia (AEMK). [provided by RefSeq, Jul 2008]
KCNA1 Gene-Disease associations (from GenCC):
- episodic ataxia type 1Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, Orphanet, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- episodic kinesigenic dyskinesia 1Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- isolated autosomal dominant hypomagnesemia, Glaudemans typeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- genetic developmental and epileptic encephalopathyInheritance: AR, AD Classification: SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000225 AC: 1AN: 445006Hom.: 0 Cov.: 0 AF XY: 0.00000426 AC XY: 1AN XY: 234576 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
445006
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
234576
show subpopulations
African (AFR)
AF:
AC:
0
AN:
12294
American (AMR)
AF:
AC:
0
AN:
18428
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13584
East Asian (EAS)
AF:
AC:
0
AN:
30838
South Asian (SAS)
AF:
AC:
0
AN:
45398
European-Finnish (FIN)
AF:
AC:
0
AN:
29212
Middle Eastern (MID)
AF:
AC:
0
AN:
1946
European-Non Finnish (NFE)
AF:
AC:
0
AN:
267460
Other (OTH)
AF:
AC:
1
AN:
25846
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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