chr7-120274665-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP6_ModerateBS2
The NM_012281.3(KCND2):c.33T>G(p.Phe11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00018 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Consequence
NM_012281.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCND2 | NM_012281.3 | c.33T>G | p.Phe11Leu | missense_variant | 1/6 | ENST00000331113.9 | |
KCND2 | XM_047420346.1 | c.33T>G | p.Phe11Leu | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCND2 | ENST00000331113.9 | c.33T>G | p.Phe11Leu | missense_variant | 1/6 | 1 | NM_012281.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250032Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135656
GnomAD4 exome AF: 0.000188 AC: 275AN: 1461798Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 117AN XY: 727210
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74300
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at