rs35131566
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001378969.1(KCND3):c.633G>T(p.Pro211=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,613,608 control chromosomes in the GnomAD database, including 1 homozygotes. 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. P211P) has been classified as Likely benign.
Frequency
Consequence
NM_001378969.1 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCND3 | NM_001378969.1 | c.633G>T | p.Pro211= | synonymous_variant | 2/8 | ENST00000302127.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCND3 | ENST00000302127.5 | c.633G>T | p.Pro211= | synonymous_variant | 2/8 | 5 | NM_001378969.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000652 AC: 99AN: 151832Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000180 AC: 45AN: 249696Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135380
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461658Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727152
GnomAD4 genome ? AF: 0.000678 AC: 103AN: 151950Hom.: 1 Cov.: 32 AF XY: 0.000620 AC XY: 46AN XY: 74250
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 07, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 14, 2018 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 02, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Spinocerebellar ataxia type 19/22 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at