rs763912060
Your query was ambiguous. Multiple possible variants found:
- chr1-110601828-G-GTGTA
- chr1-110601828-G-GTGTATA
- chr1-110601828-G-GTGTGTA
- chr1-110601828-G-GTGTGTATA
- chr1-110601828-G-GTGTGTC
- chr1-110601828-G-GTGTGTGTA
- chr1-110601828-G-GTGTGTGTATA
- chr1-110601828-G-GTGTGTGTGTA
- chr1-110601828-G-GTGTGTGTGTATA
- chr1-110601828-G-GTGTGTGTGTGTA
- chr1-110601828-G-GTGTGTGTGTGTGTA
- chr1-110601828-G-GTGTGTGTGTGTGTGTA
- chr1-110601828-G-GTGTGTGTGTGTGTGTGTA
- chr1-110601828-G-GTGTGTGTGTGTGTGTGTGTA
- chr1-110601828-G-GTGTGTGTGTGTGTGTGTGTGTA
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2
The NM_004974.4(KCNA2):c.*1454_*1455insTACA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,237,206 control chromosomes in the GnomAD database, including 14 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0044 ( 12 hom., cov: 28)
Exomes 𝑓: 0.0013 ( 2 hom. )
Consequence
KCNA2
NM_004974.4 3_prime_UTR
NM_004974.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0600
Publications
0 publications found
Genes affected
KCNA2 (HGNC:6220): (potassium voltage-gated channel subfamily A member 2) Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shaker-related subfamily. This member contains six membrane-spanning domains with a shaker-type repeat in the fourth segment. It belongs to the delayed rectifier class, members of which allow nerve cells to efficiently repolarize following an action potential. The coding region of this gene is intronless, and the gene is clustered with genes KCNA3 and KCNA10 on chromosome 1. [provided by RefSeq, Jul 2008]
KCNA2 Gene-Disease associations (from GenCC):
- developmental and epileptic encephalopathy, 32Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- undetermined early-onset epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00437 (628/143554) while in subpopulation EAS AF = 0.0451 (202/4476). AF 95% confidence interval is 0.04. There are 12 homozygotes in GnomAd4. There are 311 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.
BS2
High AC in GnomAd4 at 628 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004974.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KCNA2 | NM_004974.4 | MANE Select | c.*1454_*1455insTACA | 3_prime_UTR | Exon 3 of 3 | NP_004965.1 | P16389-1 | ||
| KCNA2 | NM_001204269.2 | c.1035+201_1035+202insTACA | intron | N/A | NP_001191198.1 | P16389-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KCNA2 | ENST00000316361.10 | TSL:2 MANE Select | c.*1454_*1455insTACA | 3_prime_UTR | Exon 3 of 3 | ENSP00000314520.4 | P16389-1 | ||
| KCNA2 | ENST00000369770.7 | TSL:1 | c.1035+201_1035+202insTACA | intron | N/A | ENSP00000358785.3 | P16389-2 | ||
| KCNA2 | ENST00000633222.1 | TSL:5 | c.*1454_*1455insTACA | 3_prime_UTR | Exon 3 of 3 | ENSP00000487785.1 | P16389-1 |
Frequencies
GnomAD3 genomes 0.00433 AC: 621AN: 143478Hom.: 11 Cov.: 28 show subpopulations
GnomAD3 genomes
AF:
AC:
621
AN:
143478
Hom.:
Cov.:
28
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00133 AC: 1458AN: 1093652Hom.: 2 Cov.: 27 AF XY: 0.00138 AC XY: 726AN XY: 524810 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1458
AN:
1093652
Hom.:
Cov.:
27
AF XY:
AC XY:
726
AN XY:
524810
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
20
AN:
22580
American (AMR)
AF:
AC:
100
AN:
10702
Ashkenazi Jewish (ASJ)
AF:
AC:
19
AN:
16024
East Asian (EAS)
AF:
AC:
629
AN:
22408
South Asian (SAS)
AF:
AC:
41
AN:
36076
European-Finnish (FIN)
AF:
AC:
74
AN:
22514
Middle Eastern (MID)
AF:
AC:
3
AN:
3068
European-Non Finnish (NFE)
AF:
AC:
497
AN:
915428
Other (OTH)
AF:
AC:
75
AN:
44852
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.324
Heterozygous variant carriers
0
96
191
287
382
478
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00437 AC: 628AN: 143554Hom.: 12 Cov.: 28 AF XY: 0.00447 AC XY: 311AN XY: 69500 show subpopulations
GnomAD4 genome
AF:
AC:
628
AN:
143554
Hom.:
Cov.:
28
AF XY:
AC XY:
311
AN XY:
69500
show subpopulations
African (AFR)
AF:
AC:
106
AN:
38368
American (AMR)
AF:
AC:
127
AN:
13926
Ashkenazi Jewish (ASJ)
AF:
AC:
13
AN:
3420
East Asian (EAS)
AF:
AC:
202
AN:
4476
South Asian (SAS)
AF:
AC:
13
AN:
4390
European-Finnish (FIN)
AF:
AC:
32
AN:
9468
Middle Eastern (MID)
AF:
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
AC:
128
AN:
66324
Other (OTH)
AF:
AC:
7
AN:
1996
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.410
Heterozygous variant carriers
0
24
47
71
94
118
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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