rs149432408
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001282684.2(KCTD17):c.390+6G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,612,104 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 1 hom. )
Consequence
KCTD17
NM_001282684.2 splice_donor_region, intron
NM_001282684.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00003988
2
Clinical Significance
Conservation
PhyloP100: 1.40
Genes affected
KCTD17 (HGNC:25705): (potassium channel tetramerization domain containing 17) This gene encodes a protein that belongs to a conserved family of potassium channel tetramerization domain (KCTD)-containing proteins. The encoded protein functions in ciliogenesis by acting as a substrate adaptor for the cullin3-based ubiquitin-conjugating enzyme E3 ligase, and targets trichoplein, a keratin-binding protein, for degradation via polyubiquitinylation. A mutation in this gene is associated with autosomal dominant myoclonic dystonia 26. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 22-37056417-G-A is Benign according to our data. Variant chr22-37056417-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 542657.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 162 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD17 | NM_001282684.2 | c.390+6G>A | splice_donor_region_variant, intron_variant | ENST00000403888.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD17 | ENST00000403888.8 | c.390+6G>A | splice_donor_region_variant, intron_variant | 1 | NM_001282684.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 162AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000862 AC: 215AN: 249390Hom.: 0 AF XY: 0.000830 AC XY: 112AN XY: 134868
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GnomAD4 exome AF: 0.00170 AC: 2477AN: 1459782Hom.: 1 Cov.: 29 AF XY: 0.00166 AC XY: 1208AN XY: 726166
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GnomAD4 genome AF: 0.00106 AC: 162AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000967 AC XY: 72AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Myoclonic dystonia 26 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at