rs761977947
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004519.4(KCNQ3):āc.183C>Gā(p.Ala61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000376 in 1,594,954 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. A61A) has been classified as Likely benign.
Frequency
Consequence
NM_004519.4 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 |
---|---|---|---|---|---|---|---|
KCNQ3 | NM_004519.4 | c.183C>G | p.Ala61= | synonymous_variant | 1/15 | ENST00000388996.10 | |
KCNQ3 | XM_047421769.1 | c.183C>G | p.Ala61= | synonymous_variant | 1/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ3 | ENST00000388996.10 | c.183C>G | p.Ala61= | synonymous_variant | 1/15 | 1 | NM_004519.4 | P1 | |
KCNQ3 | ENST00000519445.5 | c.183C>G | p.Ala61= | synonymous_variant | 1/15 | 5 | |||
KCNQ3 | ENST00000519589.1 | upstream_gene_variant | 2 | ||||||
KCNQ3 | ENST00000639358.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151728Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000913 AC: 2AN: 219102Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120714
GnomAD4 exome AF: 0.00000346 AC: 5AN: 1443226Hom.: 0 Cov.: 33 AF XY: 0.00000279 AC XY: 2AN XY: 717484
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151728Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74068
ClinVar
Submissions by phenotype
Benign neonatal seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at