rs118192252
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004519.4(KCNQ3):c.1403A>G(p.Asn468Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000545 in 1,614,220 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N468K) has been classified as Uncertain significance.
Frequency
Consequence
NM_004519.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ3 | NM_004519.4 | c.1403A>G | p.Asn468Ser | missense_variant | 10/15 | ENST00000388996.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ3 | ENST00000388996.10 | c.1403A>G | p.Asn468Ser | missense_variant | 10/15 | 1 | NM_004519.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251480Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135910
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727244
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74500
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 08, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 03, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 25, 2019 | This variant is associated with the following publications: (PMID: 14534157, 32613771) - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2019 | 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. - |
Benign neonatal seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Seizures, benign familial neonatal, 2 Other:1
not provided, no classification provided | literature only | GeneReviews | - | All 3 sibs with the variant were affected. Chinese ethnicity; variant is present in 0.06% of East Asians (gnomAD) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at