18-26564147-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001258222.3(KCTD1):c.10-62897G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,834 control chromosomes in the GnomAD database, including 9,245 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 0.33 ( 9245 hom., cov: 31)
Consequence
KCTD1
NM_001258222.3 intron
NM_001258222.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.217
Genes affected
KCTD1 (HGNC:18249): (potassium channel tetramerization domain containing 1) This gene encodes a protein containing a BTB (Broad-complex, tramtrack and bric a brac), also known as a POZ (POxvirus and zinc finger) protein-protein interaction domain. The encoded protein negatively regulates the AP-2 family of transcription factors and the Wnt signaling pathway. A mechanism for the modulation of Wnt signaling has been proposed in which the encoded protein enhances ubiquitination and degradation of the beta-catenin protein. Mutations in this gene have been identified in Scalp-ear-nipple (SEN) syndrome. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCTD1 | NM_001258222.3 | c.10-62897G>A | intron_variant | Intron 1 of 4 | NP_001245151.1 | |||
KCTD1 | NM_198991.4 | c.-15-62897G>A | intron_variant | Intron 2 of 5 | NP_945342.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCTD1 | ENST00000579973.5 | c.-15-62897G>A | intron_variant | Intron 2 of 5 | 1 | ENSP00000464170.1 | ||||
KCTD1 | ENST00000580191.5 | c.10-62897G>A | intron_variant | Intron 1 of 4 | 2 | ENSP00000464261.1 | ||||
KCTD1 | ENST00000317932.11 | c.-15-62897G>A | intron_variant | Intron 1 of 4 | 5 | ENSP00000314831.7 |
Frequencies
GnomAD3 genomes AF: 0.328 AC: 49797AN: 151716Hom.: 9240 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.328 AC: 49825AN: 151834Hom.: 9245 Cov.: 31 AF XY: 0.331 AC XY: 24531AN XY: 74186
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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