chr1-110603598-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004974.4(KCNA2):c.1185G>A(p.Ala395Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,613,964 control chromosomes in the GnomAD database, including 4 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. A395A) has been classified as Benign.
Frequency
Consequence
NM_004974.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000394 AC: 99AN: 251392Hom.: 2 AF XY: 0.000228 AC XY: 31AN XY: 135872
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461792Hom.: 4 Cov.: 34 AF XY: 0.0000509 AC XY: 37AN XY: 727202
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74396
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 32 Benign:1
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Inborn genetic diseases Benign:1
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. -
not provided Benign:1
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KCNA2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at