19-50314777-TCCCCACC-TCCCCACCCCCCACC
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_004977.3(KCNC3):c.*1331_*1337dupGGTGGGG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000037 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KCNC3
NM_004977.3 3_prime_UTR
NM_004977.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.26
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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.*1331_*1337dupGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000477616.2 | NP_004968.2 | ||
KCNC3 | NM_001372305.1 | c.*1331_*1337dupGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | NP_001359234.1 | |||
KCNC3 | NR_110912.2 | n.526_532dupGGTGGGG | non_coding_transcript_exon_variant | Exon 4 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616 | c.*1331_*1337dupGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_004977.3 | ENSP00000434241.1 | |||
KCNC3 | ENST00000670667 | c.*70_*76dupGGTGGGG | 3_prime_UTR_variant | Exon 4 of 4 | ENSP00000499301.1 | |||||
KCNC3 | ENST00000376959 | c.*249_*255dupGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | 5 | ENSP00000366158.2 | ||||
KCNC3 | ENST00000474951 | c.*249_*255dupGGTGGGG | 3_prime_UTR_variant | Exon 4 of 4 | 2 | ENSP00000432438.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 151794Hom.: 0 Cov.: 31 FAILED QC
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GnomAD4 exome AF: 0.00000371 AC: 1AN: 269720Hom.: 0 Cov.: 0 AF XY: 0.00000645 AC XY: 1AN XY: 155020
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000659 AC: 1AN: 151794Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74156
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at