chr18-26455940-GTAAGTCC-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001142730.3(KCTD1):c.2440-46_2440-40del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 1,599,592 control chromosomes in the GnomAD database, including 2,113 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.053 ( 257 hom., cov: 31)
Exomes 𝑓: 0.049 ( 1856 hom. )
Consequence
KCTD1
NM_001142730.3 intron
NM_001142730.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.802
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 -10 ACMG points.
BP6
?
Variant 18-26455940-GTAAGTCC-G is Benign according to our data. Variant chr18-26455940-GTAAGTCC-G is described in ClinVar as [Benign]. Clinvar id is 1232178.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0653 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD1 | NM_001142730.3 | c.2440-46_2440-40del | intron_variant | ENST00000580059.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD1 | ENST00000580059.7 | c.2440-46_2440-40del | intron_variant | 3 | NM_001142730.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0532 AC: 8100AN: 152144Hom.: 256 Cov.: 31
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GnomAD3 exomes AF: 0.0459 AC: 11081AN: 241270Hom.: 290 AF XY: 0.0447 AC XY: 5838AN XY: 130598
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GnomAD4 exome AF: 0.0489 AC: 70725AN: 1447330Hom.: 1856 AF XY: 0.0479 AC XY: 34385AN XY: 718232
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GnomAD4 genome ? AF: 0.0532 AC: 8104AN: 152262Hom.: 257 Cov.: 31 AF XY: 0.0537 AC XY: 4001AN XY: 74442
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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 16, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at