chr11-2445106-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4
The NM_000218.3(KCNQ1):c.8C>G(p.Ala3Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000106 in 942,112 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A3P) has been classified as Uncertain significance.
Frequency
Consequence
NM_000218.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.8C>G | p.Ala3Gly | missense_variant | 1/16 | ENST00000155840.12 | |
KCNQ1 | NM_001406836.1 | c.8C>G | p.Ala3Gly | missense_variant | 1/15 | ||
KCNQ1 | NM_001406838.1 | c.8C>G | p.Ala3Gly | missense_variant | 1/11 | ||
KCNQ1 | NM_001406837.1 | c.-355C>G | 5_prime_UTR_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.8C>G | p.Ala3Gly | missense_variant | 1/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000646564.2 | c.8C>G | p.Ala3Gly | missense_variant | 1/11 | ||||
KCNQ1 | ENST00000496887.7 | c.24-277C>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000106 AC: 1AN: 942112Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 443926
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at