chr7-120745785-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_012281.3(KCND2):c.1473C>T(p.His491=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000225 in 1,613,584 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 1 hom. )
Consequence
KCND2
NM_012281.3 synonymous
NM_012281.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
Genes affected
KCND2 (HGNC:6238): (potassium voltage-gated channel subfamily D member 2) 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 mediates a rapidly inactivating, A-type outward potassium current which is not under the control of the N terminus as it is in Shaker channels. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 7-120745785-C-T is Benign according to our data. Variant chr7-120745785-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 460199.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.15 with no splicing effect.
BS2
High AC in GnomAd4 at 181 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCND2 | NM_012281.3 | c.1473C>T | p.His491= | synonymous_variant | 5/6 | ENST00000331113.9 | |
KCND2 | XM_047420346.1 | c.1473C>T | p.His491= | synonymous_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCND2 | ENST00000331113.9 | c.1473C>T | p.His491= | synonymous_variant | 5/6 | 1 | NM_012281.3 | P1 | |
KCND2 | ENST00000425288.1 | c.231C>T | p.His77= | synonymous_variant | 4/5 | 4 | |||
KCND2 | ENST00000473190.1 | n.288C>T | non_coding_transcript_exon_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00117 AC: 178AN: 152158Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000383 AC: 96AN: 250540Hom.: 0 AF XY: 0.000303 AC XY: 41AN XY: 135404
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GnomAD4 exome AF: 0.000125 AC: 182AN: 1461308Hom.: 1 Cov.: 32 AF XY: 0.000113 AC XY: 82AN XY: 726962
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GnomAD4 genome AF: 0.00119 AC: 181AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.00129 AC XY: 96AN XY: 74444
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
KCND2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 17, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Early myoclonic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at