rs554197864
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004977.3(KCNC3):c.1760C>T(p.Pro587Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000378 in 1,523,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P587R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004977.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.1760C>T | p.Pro587Leu | missense_variant | 2/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | c.1532C>T | p.Pro511Leu | missense_variant | 2/5 | ||
KCNC3 | NR_110912.2 | n.69-2409C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.1760C>T | p.Pro587Leu | missense_variant | 2/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000670667.1 | c.1760C>T | p.Pro587Leu | missense_variant | 2/4 | P3 | |||
KCNC3 | ENST00000376959.6 | c.1760C>T | p.Pro587Leu | missense_variant | 2/5 | 5 | A2 | ||
KCNC3 | ENST00000474951.1 | c.-74-2409C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000133 AC: 18AN: 135648Hom.: 0 AF XY: 0.000121 AC XY: 9AN XY: 74350
GnomAD4 exome AF: 0.000400 AC: 549AN: 1370894Hom.: 0 Cov.: 30 AF XY: 0.000366 AC XY: 248AN XY: 677006
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74478
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 30, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at