rs571327522
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_004977.3(KCNC3):c.1032G>A(p.Thr344=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,060 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T344T) has been classified as Likely benign.
Frequency
Consequence
NM_004977.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.1032G>A | p.Thr344= | synonymous_variant | 2/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | c.804G>A | p.Thr268= | synonymous_variant | 2/5 | ||
KCNC3 | NR_110912.2 | n.69-3137G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.1032G>A | p.Thr344= | synonymous_variant | 2/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000670667.1 | c.1032G>A | p.Thr344= | synonymous_variant | 2/4 | P3 | |||
KCNC3 | ENST00000376959.6 | c.1032G>A | p.Thr344= | synonymous_variant | 2/5 | 5 | A2 | ||
KCNC3 | ENST00000474951.1 | c.-74-3137G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251382Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135892
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461888Hom.: 0 Cov.: 34 AF XY: 0.0000371 AC XY: 27AN XY: 727244
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74338
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 02, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at