chr19-50314777-TCCCCACC-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004977.3(KCNC3):c.*1331_*1337delGGTGGGG variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00000659 in 151,794 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004977.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.*1331_*1337delGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000477616.2 | NP_004968.2 | ||
KCNC3 | NM_001372305.1 | c.*1331_*1337delGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | NP_001359234.1 | |||
KCNC3 | NR_110912.2 | n.526_532delGGTGGGG | 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_*1337delGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_004977.3 | ENSP00000434241.1 | |||
KCNC3 | ENST00000670667 | c.*70_*76delGGTGGGG | 3_prime_UTR_variant | Exon 4 of 4 | ENSP00000499301.1 | |||||
KCNC3 | ENST00000376959 | c.*249_*255delGGTGGGG | 3_prime_UTR_variant | Exon 5 of 5 | 5 | ENSP00000366158.2 | ||||
KCNC3 | ENST00000474951 | c.*249_*255delGGTGGGG | 3_prime_UTR_variant | Exon 4 of 4 | 2 | ENSP00000432438.1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151794Hom.: 0 Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 269716Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 155018
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151794Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74156
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: KCNC3 c.*1331_*1337delGGTGGGG is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 2.4e-06 in 421510 control chromosomes (gnomAD v4.0). The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. To our knowledge, no occurrence of c.*1331_*1337delGGTGGGG in individuals affected with Spinocerebellar Ataxia Type 13 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at