rs1001882554
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004977.3(KCNC3):c.1752G>A(p.Pro584=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000469 in 938,598 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000060 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000044 ( 1 hom. )
Consequence
KCNC3
NM_004977.3 synonymous
NM_004977.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.604
Genes affected
KCNC3 (HGNC:6235): (potassium voltage-gated channel subfamily C member 3) The Shaker gene family of Drosophila encodes components of voltage-gated potassium channels and is comprised of four subfamilies. Based on sequence similarity, this gene is similar to one of these subfamilies, namely the Shaw subfamily. The protein encoded by this gene belongs to the delayed rectifier class of channel proteins and is an integral membrane protein that mediates the voltage-dependent potassium ion permeability of excitable membranes. Alternate splicing results in several transcript variants. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 19-50323201-C-T is Benign according to our data. Variant chr19-50323201-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 586082.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.604 with no splicing effect.
BS2
?
High AC in GnomAd4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.1752G>A | p.Pro584= | synonymous_variant | 2/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | c.1524G>A | p.Pro508= | synonymous_variant | 2/5 | ||
KCNC3 | NR_110912.2 | n.69-2417G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.1752G>A | p.Pro584= | synonymous_variant | 2/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000670667.1 | c.1752G>A | p.Pro584= | synonymous_variant | 2/4 | P3 | |||
KCNC3 | ENST00000376959.6 | c.1752G>A | p.Pro584= | synonymous_variant | 2/5 | 5 | A2 | ||
KCNC3 | ENST00000474951.1 | c.-74-2417G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000601 AC: 9AN: 149666Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000822 AC: 11AN: 133782Hom.: 1 AF XY: 0.000123 AC XY: 9AN XY: 73368
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GnomAD4 exome AF: 0.0000444 AC: 35AN: 788932Hom.: 1 Cov.: 24 AF XY: 0.0000491 AC XY: 20AN XY: 407296
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GnomAD4 genome ? AF: 0.0000601 AC: 9AN: 149666Hom.: 0 Cov.: 32 AF XY: 0.0000684 AC XY: 5AN XY: 73082
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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
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 14, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2023 | - - |
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