7-120274701-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_012281.3(KCND2):āc.69C>Gā(p.Ala23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,794 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. A23A) has been classified as Likely benign.
Frequency
Consequence
NM_012281.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCND2 | NM_012281.3 | c.69C>G | p.Ala23= | synonymous_variant | 1/6 | ENST00000331113.9 | |
KCND2 | XM_047420346.1 | c.69C>G | p.Ala23= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCND2 | ENST00000331113.9 | c.69C>G | p.Ala23= | synonymous_variant | 1/6 | 1 | NM_012281.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250748Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135726
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461726Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727164
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74256
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at