chr1-110601792-A-ATG
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004974.4(KCNA2):c.*1490_*1491insCA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 139,420 control chromosomes in the GnomAD database, including 41 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.022 ( 41 hom., cov: 29)
Exomes 𝑓: 0.012 ( 3 hom. )
Failed GnomAD Quality Control
Consequence
KCNA2
NM_004974.4 3_prime_UTR
NM_004974.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.89
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 1-110601792-A-ATG is Benign according to our data. Variant chr1-110601792-A-ATG is described in ClinVar as [Likely_benign]. Clinvar id is 1201388.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0216 (3006/139420) while in subpopulation NFE AF= 0.0281 (1847/65822). AF 95% confidence interval is 0.027. There are 41 homozygotes in gnomad4. There are 1498 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3006 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNA2 | NM_004974.4 | c.*1490_*1491insCA | 3_prime_UTR_variant | 3/3 | ENST00000316361.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNA2 | ENST00000316361.10 | c.*1490_*1491insCA | 3_prime_UTR_variant | 3/3 | 2 | NM_004974.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0216 AC: 3003AN: 139322Hom.: 41 Cov.: 29
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0121 AC: 11608AN: 959578Hom.: 3 Cov.: 18 AF XY: 0.0124 AC XY: 5626AN XY: 454412
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.0216 AC: 3006AN: 139420Hom.: 41 Cov.: 29 AF XY: 0.0222 AC XY: 1498AN XY: 67548
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 22, 2020 | - - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at