chr11-17779535-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001112741.2(KCNC1):c.1584C>T(p.Pro528=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,551,206 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 Benign (★). Synonymous variant affecting the same amino acid position (i.e. P528P) has been classified as Likely benign.
Frequency
Consequence
NM_001112741.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC1 | NM_001112741.2 | c.1584C>T | p.Pro528= | synonymous_variant | 3/4 | ENST00000265969.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC1 | ENST00000265969.8 | c.1584C>T | p.Pro528= | synonymous_variant | 3/4 | 5 | NM_001112741.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152170Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000267 AC: 41AN: 153810Hom.: 0 AF XY: 0.000282 AC XY: 23AN XY: 81600
GnomAD4 exome AF: 0.0000958 AC: 134AN: 1399036Hom.: 1 Cov.: 31 AF XY: 0.000104 AC XY: 72AN XY: 690044
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152170Hom.: 1 Cov.: 33 AF XY: 0.000377 AC XY: 28AN XY: 74330
ClinVar
Submissions by phenotype
Progressive myoclonic epilepsy type 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at