chrX-117909566-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001168302.2(KLHL13):āc.1053T>Cā(p.His351=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,209,907 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000063 ( 0 hom., 3 hem., cov: 24)
Exomes š: 0.0000018 ( 0 hom. 1 hem. )
Consequence
KLHL13
NM_001168302.2 synonymous
NM_001168302.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.41
Genes affected
KLHL13 (HGNC:22931): (kelch like family member 13) This gene encodes a BTB and kelch domain containing protein and belongs to the kelch repeat domain containing superfamily of proteins. The encoded protein functions as an adaptor protein that complexes with Cullin 3 and other proteins to form the Cullin 3-based E3 ubiquitin-protein ligase complex. This complex is necessary for proper chromosome segregation and completion of cytokinesis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
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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=-0.58).
BP6
Variant X-117909566-A-G is Benign according to our data. Variant chrX-117909566-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2661258.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.41 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL13 | NM_001168302.2 | c.1053T>C | p.His351= | synonymous_variant | 6/8 | ENST00000540167.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL13 | ENST00000540167.6 | c.1053T>C | p.His351= | synonymous_variant | 6/8 | 2 | NM_001168302.2 |
Frequencies
GnomAD3 genomes AF: 0.0000627 AC: 7AN: 111727Hom.: 0 Cov.: 24 AF XY: 0.0000885 AC XY: 3AN XY: 33903
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GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098180Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 1AN XY: 363536
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GnomAD4 genome AF: 0.0000627 AC: 7AN: 111727Hom.: 0 Cov.: 24 AF XY: 0.0000885 AC XY: 3AN XY: 33903
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | KLHL13: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at