rs141110759
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015443.4(KANSL1):c.635A>G(p.His212Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000426 in 1,614,086 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H212P) has been classified as Likely benign.
Frequency
Consequence
NM_015443.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KANSL1 | NM_015443.4 | c.635A>G | p.His212Arg | missense_variant | 2/15 | ENST00000432791.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.635A>G | p.His212Arg | missense_variant | 2/15 | 1 | NM_015443.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152200Hom.: 1 Cov.: 35
GnomAD3 exomes AF: 0.000374 AC: 94AN: 251286Hom.: 1 AF XY: 0.000361 AC XY: 49AN XY: 135814
GnomAD4 exome AF: 0.000429 AC: 627AN: 1461768Hom.: 1 Cov.: 35 AF XY: 0.000481 AC XY: 350AN XY: 727176
GnomAD4 genome ? AF: 0.000400 AC: 61AN: 152318Hom.: 1 Cov.: 35 AF XY: 0.000376 AC XY: 28AN XY: 74484
ClinVar
Submissions by phenotype
Koolen-de Vries syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 19, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 16, 2021 | This variant is associated with the following publications: (PMID: 22544363, 29352316) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at