rs759846708
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000432791.7(KANSL1):āc.531T>Cā(p.Asn177=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,578,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 35)
Exomes š: 0.000016 ( 0 hom. )
Consequence
KANSL1
ENST00000432791.7 synonymous
ENST00000432791.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.55
Genes affected
KANSL1 (HGNC:24565): (KAT8 regulatory NSL complex subunit 1) This gene encodes a nuclear protein that is a subunit of two protein complexes involved with histone acetylation, the MLL1 complex and the NSL1 complex. The encoded protein has been implicated in a variety of cellular processes including enhancer regulation, cell proliferation, and mitosis. Mutations in this gene are associated with Koolen-de Vries Syndrome. [provided by RefSeq, May 2022]
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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 17-46171613-A-G is Benign according to our data. Variant chr17-46171613-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 468410.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.55 with no splicing effect.
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KANSL1 | NM_015443.4 | c.531T>C | p.Asn177= | synonymous_variant | 2/15 | ENST00000432791.7 | NP_056258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.531T>C | p.Asn177= | synonymous_variant | 2/15 | 1 | NM_015443.4 | ENSP00000387393 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152024Hom.: 0 Cov.: 35
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GnomAD3 exomes AF: 0.00000918 AC: 2AN: 217894Hom.: 0 AF XY: 0.00000848 AC XY: 1AN XY: 117918
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GnomAD4 exome AF: 0.0000161 AC: 23AN: 1426004Hom.: 0 Cov.: 35 AF XY: 0.0000170 AC XY: 12AN XY: 707890
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152024Hom.: 0 Cov.: 35 AF XY: 0.0000539 AC XY: 4AN XY: 74242
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Koolen-de Vries syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 18, 2023 | - - |
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