chr18-26459525-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001142730.3(KCTD1):c.2439+95T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 1,223,688 control chromosomes in the GnomAD database, including 528,834 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.92 ( 64216 hom., cov: 33)
Exomes 𝑓: 0.93 ( 464618 hom. )
Consequence
KCTD1
NM_001142730.3 intron
NM_001142730.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.651
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 18-26459525-A-C is Benign according to our data. Variant chr18-26459525-A-C is described in ClinVar as [Benign]. Clinvar id is 1282752.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD1 | NM_001142730.3 | c.2439+95T>G | intron_variant | ENST00000580059.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD1 | ENST00000580059.7 | c.2439+95T>G | intron_variant | 3 | NM_001142730.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.918 AC: 139687AN: 152186Hom.: 64169 Cov.: 33
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GnomAD4 exome AF: 0.931 AC: 997438AN: 1071384Hom.: 464618 Cov.: 14 AF XY: 0.930 AC XY: 496401AN XY: 533978
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GnomAD4 genome ? AF: 0.918 AC: 139795AN: 152304Hom.: 64216 Cov.: 33 AF XY: 0.917 AC XY: 68308AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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