rs116768044
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004977.3(KCNC3):c.1563G>T(p.Ala521=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A521A) has been classified as Benign.
Frequency
Consequence
NM_004977.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.1563G>T | p.Ala521= | synonymous_variant | 2/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | c.1335G>T | p.Ala445= | synonymous_variant | 2/5 | ||
KCNC3 | NR_110912.2 | n.69-2606G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.1563G>T | p.Ala521= | synonymous_variant | 2/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000670667.1 | c.1563G>T | p.Ala521= | synonymous_variant | 2/4 | P3 | |||
KCNC3 | ENST00000376959.6 | c.1563G>T | p.Ala521= | synonymous_variant | 2/5 | 5 | A2 | ||
KCNC3 | ENST00000474951.1 | c.-74-2606G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251358Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461840Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727226
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at