rs694997
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2
The NM_138444.4(KCTD12):c.216G>A(p.Leu72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,593,870 control chromosomes in the GnomAD database, including 40 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 0.0079 ( 17 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 23 hom. )
Consequence
KCTD12
NM_138444.4 synonymous
NM_138444.4 synonymous
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.56
Genes affected
KCTD12 (HGNC:14678): (potassium channel tetramerization domain containing 12) Enables identical protein binding activity. Predicted to be involved in protein homooligomerization. Predicted to act upstream of or within regulation of G protein-coupled receptor signaling pathway. Predicted to be located in cell projection. Predicted to be part of receptor complex. Predicted to be active in postsynaptic membrane and presynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP7
?
Synonymous conserved (PhyloP=3.56 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00789 (1202/152358) while in subpopulation AFR AF= 0.0265 (1104/41584). AF 95% confidence interval is 0.0252. There are 17 homozygotes in gnomad4. There are 592 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 17 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD12 | NM_138444.4 | c.216G>A | p.Leu72= | synonymous_variant | 1/1 | ENST00000377474.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD12 | ENST00000377474.4 | c.216G>A | p.Leu72= | synonymous_variant | 1/1 | NM_138444.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00787 AC: 1198AN: 152240Hom.: 17 Cov.: 33
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GnomAD3 exomes AF: 0.00264 AC: 578AN: 218790Hom.: 5 AF XY: 0.00207 AC XY: 252AN XY: 121498
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GnomAD4 exome AF: 0.00114 AC: 1647AN: 1441512Hom.: 23 Cov.: 31 AF XY: 0.00102 AC XY: 730AN XY: 717402
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GnomAD4 genome ? AF: 0.00789 AC: 1202AN: 152358Hom.: 17 Cov.: 33 AF XY: 0.00795 AC XY: 592AN XY: 74504
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at