rs138175526
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015443.4(KANSL1):c.607G>T(p.Gly203Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,612,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 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. G203R) has been classified as Uncertain significance.
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.607G>T | p.Gly203Trp | missense_variant | 2/15 | ENST00000432791.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.607G>T | p.Gly203Trp | missense_variant | 2/15 | 1 | NM_015443.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152110Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.000273 AC: 68AN: 249330Hom.: 0 AF XY: 0.000371 AC XY: 50AN XY: 134840
GnomAD4 exome AF: 0.000136 AC: 199AN: 1460270Hom.: 0 Cov.: 35 AF XY: 0.000197 AC XY: 143AN XY: 726454
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152228Hom.: 0 Cov.: 35 AF XY: 0.000134 AC XY: 10AN XY: 74420
ClinVar
Submissions by phenotype
Koolen-de Vries syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 07, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 22, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at