rs778178483
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000432791.7(KANSL1):c.1652C>T(p.Thr551Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,547,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T551S) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000432791.7 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KANSL1 | NM_015443.4 | c.1652C>T | p.Thr551Ile | missense_variant, splice_region_variant | 5/15 | ENST00000432791.7 | NP_056258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.1652C>T | p.Thr551Ile | missense_variant, splice_region_variant | 5/15 | 1 | NM_015443.4 | ENSP00000387393 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000283 AC: 71AN: 250904Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135586
GnomAD4 exome AF: 0.0000795 AC: 111AN: 1395552Hom.: 0 Cov.: 25 AF XY: 0.0000673 AC XY: 47AN XY: 698098
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
Koolen-de Vries syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | KANSL1 NM_001193466.1 exon 5 p.Thr551Ile (c.1652C>T): This variant has not been reported in the literature but is present in 0.1% (43/34332) of Latino alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs778178483). This variant is present in ClinVar (Variation ID:379763). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 04, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 21, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at