chr1-110593989-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004974.4(KCNA2):c.*9294C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 1,545,932 control chromosomes in the GnomAD database, including 11,449 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.095 ( 1333 hom., cov: 30)
Exomes 𝑓: 0.087 ( 10116 hom. )
Consequence
KCNA2
NM_004974.4 3_prime_UTR
NM_004974.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.795
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 1-110593989-G-A is Benign according to our data. Variant chr1-110593989-G-A is described in ClinVar as [Benign]. Clinvar id is 1257086.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNA2 | NM_004974.4 | c.*9294C>T | 3_prime_UTR_variant | 3/3 | ENST00000316361.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNA2 | ENST00000316361.10 | c.*9294C>T | 3_prime_UTR_variant | 3/3 | 2 | NM_004974.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0953 AC: 14474AN: 151948Hom.: 1333 Cov.: 30
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GnomAD4 exome AF: 0.0868 AC: 120964AN: 1393866Hom.: 10116 Cov.: 31 AF XY: 0.0887 AC XY: 60978AN XY: 687442
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GnomAD4 genome ? AF: 0.0952 AC: 14477AN: 152066Hom.: 1333 Cov.: 30 AF XY: 0.105 AC XY: 7779AN XY: 74332
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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 | Jul 15, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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