rs375737637
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004977.3(KCNC3):c.1940C>T(p.Pro647Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000387 in 1,548,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P647P) has been classified as Likely benign.
Frequency
Consequence
NM_004977.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.1940C>T | p.Pro647Leu | missense_variant | 2/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | c.1712C>T | p.Pro571Leu | missense_variant | 2/5 | ||
KCNC3 | NR_110912.2 | n.69-2229C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.1940C>T | p.Pro647Leu | missense_variant | 2/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000670667.1 | c.1940C>T | p.Pro647Leu | missense_variant | 2/4 | P3 | |||
KCNC3 | ENST00000376959.6 | c.1940C>T | p.Pro647Leu | missense_variant | 2/5 | 5 | A2 | ||
KCNC3 | ENST00000474951.1 | c.-74-2229C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000546 AC: 8AN: 146510Hom.: 0 AF XY: 0.0000507 AC XY: 4AN XY: 78926
GnomAD4 exome AF: 0.0000408 AC: 57AN: 1396298Hom.: 0 Cov.: 33 AF XY: 0.0000523 AC XY: 36AN XY: 688670
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 05, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at