rs139804857
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001112741.2(KCNC1):c.1287C>A(p.Ala429=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000246 in 1,614,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
KCNC1
NM_001112741.2 synonymous
NM_001112741.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.08
Genes affected
KCNC1 (HGNC:6233): (potassium voltage-gated channel subfamily C member 1) This gene encodes a member of a family of integral membrane proteins that mediate the voltage-dependent potassium ion permeability of excitable membranes. Alternative splicing is thought to result in two transcript variants encoding isoforms that differ at their C-termini. These isoforms have had conflicting names in the literature: the longer isoform has been called both "b" and "alpha", while the shorter isoform has been called both "a" and "beta" (PMIDs 1432046, 12091563). [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 11-17772381-C-A is Benign according to our data. Variant chr11-17772381-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 475348.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00123 (187/152338) while in subpopulation AFR AF= 0.00411 (171/41586). AF 95% confidence interval is 0.00361. There are 0 homozygotes in gnomad4. There are 76 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 187 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC1 | NM_001112741.2 | c.1287C>A | p.Ala429= | synonymous_variant | 2/4 | ENST00000265969.8 | |
KCNC1 | NM_004976.4 | c.1287C>A | p.Ala429= | synonymous_variant | 2/2 | ||
KCNC1 | XM_047426916.1 | c.1287C>A | p.Ala429= | synonymous_variant | 2/4 | ||
KCNC1 | XR_930866.3 | n.2509C>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC1 | ENST00000265969.8 | c.1287C>A | p.Ala429= | synonymous_variant | 2/4 | 5 | NM_001112741.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00123 AC: 187AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000291 AC: 73AN: 251188Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135796
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GnomAD4 exome AF: 0.000144 AC: 210AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 727234
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GnomAD4 genome ? AF: 0.00123 AC: 187AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.00102 AC XY: 76AN XY: 74490
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Progressive myoclonic epilepsy type 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | - - |
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