chr17-46039189-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015443.4(KANSL1):āc.2230G>Cā(p.Asp744His) variant causes a missense change. The variant allele was found at a frequency of 0.0000834 in 1,595,080 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 ā ). Synonymous variant affecting the same amino acid position (i.e. D744D) 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.2230G>C | p.Asp744His | missense_variant | 9/15 | ENST00000432791.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.2230G>C | p.Asp744His | missense_variant | 9/15 | 1 | NM_015443.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000196 AC: 46AN: 234240Hom.: 0 AF XY: 0.000165 AC XY: 21AN XY: 127258
GnomAD4 exome AF: 0.0000825 AC: 119AN: 1442758Hom.: 0 Cov.: 31 AF XY: 0.0000822 AC XY: 59AN XY: 717374
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74484
ClinVar
Submissions by phenotype
Koolen-de Vries syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 17, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 03, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at