rs145452045
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000218.3(KCNQ1):c.1323C>T(p.Pro441=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,334 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 (★★). Synonymous variant affecting the same amino acid position (i.e. P441P) has been classified as Likely benign.
Frequency
Consequence
NM_000218.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.1323C>T | p.Pro441= | synonymous_variant | 10/16 | ENST00000155840.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.1323C>T | p.Pro441= | synonymous_variant | 10/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000335475.6 | c.942C>T | p.Pro314= | synonymous_variant | 10/16 | 1 | |||
KCNQ1 | ENST00000496887.7 | c.966C>T | p.Pro322= | synonymous_variant | 10/16 | 5 | |||
KCNQ1 | ENST00000646564.2 | c.783C>T | p.Pro261= | synonymous_variant | 5/11 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151942Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250694Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135596
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461392Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726988
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151942Hom.: 0 Cov.: 33 AF XY: 0.0000943 AC XY: 7AN XY: 74198
ClinVar
Submissions by phenotype
Long QT syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 02, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Dec 01, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | May 16, 2016 | Variant summary: The KCNQ1 c.1323C>T (p.Pro441Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome while 5/5 in silico splice prediction algorithms predict the variant not to have an impact on splicing. This variant was observed in the African subpopulation at a frequency of 0.0001988 (2/10062). This frequency is about 2 times the estimated maximal expected allele frequency of a pathogenic KCNQ1 variant (0.0001), suggesting this is likely a benign polymorphism. To our knowledge, the variant was not reported in affected patients with strong evidence for pathogenicity. In an internal sample, the variant was observed to co-occur with a pathogenic KCNQ1 variant further supporting a neutral outcome. Taken together, this variant is classified as Likely Benign. - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2020 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at