rs640029
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378969.1(KCND3):c.1518+26A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,598,466 control chromosomes in the GnomAD database, including 33,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.22 ( 4250 hom., cov: 31)
Exomes 𝑓: 0.19 ( 28931 hom. )
Consequence
KCND3
NM_001378969.1 intron
NM_001378969.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0600
Genes affected
KCND3 (HGNC:6239): (potassium voltage-gated channel subfamily D member 3) Voltage-gated potassium (Kv) 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, shal-related subfamily, members of which form voltage-activated A-type potassium ion channels and are prominent in the repolarization phase of the action potential. This member includes two isoforms with different sizes, which are encoded by alternatively spliced transcript variants of this gene. [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=-0.53).
BP6
?
Variant 1-111778410-T-A is Benign according to our data. Variant chr1-111778410-T-A is described in ClinVar as [Benign]. Clinvar id is 1293604.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCND3 | NM_001378969.1 | c.1518+26A>T | intron_variant | ENST00000302127.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCND3 | ENST00000302127.5 | c.1518+26A>T | intron_variant | 5 | NM_001378969.1 | P3 | |||
KCND3 | ENST00000315987.6 | c.1518+26A>T | intron_variant | 1 | P3 | ||||
KCND3 | ENST00000369697.5 | c.1462-1137A>T | intron_variant | 1 | A1 | ||||
KCND3 | ENST00000703640.1 | n.2153-1137A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.224 AC: 33961AN: 151808Hom.: 4246 Cov.: 31
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GnomAD3 exomes AF: 0.173 AC: 43512AN: 251144Hom.: 4464 AF XY: 0.173 AC XY: 23482AN XY: 135762
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GnomAD4 exome AF: 0.193 AC: 279882AN: 1446540Hom.: 28931 Cov.: 29 AF XY: 0.192 AC XY: 138378AN XY: 720660
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GnomAD4 genome ? AF: 0.224 AC: 34000AN: 151926Hom.: 4250 Cov.: 31 AF XY: 0.219 AC XY: 16258AN XY: 74266
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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 | Jun 23, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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