rs2237892
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000218(KCNQ1):c.1795-29246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152038 control chromosomes in the gnomAD Genomes database, including 1182 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.096 ( 1182 hom., cov: 32)
Consequence
KCNQ1
NM_000218 intron
NM_000218 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.03
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.1795-29246C>T | intron_variant | ENST00000155840.12 | |||
KCNQ1 | NM_181798.1 | c.1414-29246C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.1795-29246C>T | intron_variant | 1 | NM_000218.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0958 AC: 14571AN: 152038Hom.: 1182 Cov.: 32
GnomAD3 genomes
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14571
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32
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Asia WGS
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685
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at