rs35450031
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_172107.4(KCNQ2):c.1689C>T(p.Asp563Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000955 in 1,613,512 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_172107.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00472 AC: 718AN: 152202Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00137 AC: 343AN: 251180Hom.: 2 AF XY: 0.00102 AC XY: 139AN XY: 135854
GnomAD4 exome AF: 0.000560 AC: 818AN: 1461192Hom.: 5 Cov.: 32 AF XY: 0.000483 AC XY: 351AN XY: 726896
GnomAD4 genome AF: 0.00475 AC: 723AN: 152320Hom.: 3 Cov.: 33 AF XY: 0.00455 AC XY: 339AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Inborn genetic diseases Benign:1
This alteration is classified as 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. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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Developmental and epileptic encephalopathy, 7 Other:1
EE (epileptic encephalopathy) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at