17-46050696-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_015443.4(KANSL1):āc.1857G>Cā(p.Arg619=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,607,388 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. R619R) has been classified as Likely benign.
Frequency
Consequence
NM_015443.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KANSL1 | NM_015443.4 | c.1857G>C | p.Arg619= | synonymous_variant | 7/15 | ENST00000432791.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.1857G>C | p.Arg619= | synonymous_variant | 7/15 | 1 | NM_015443.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248366Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 134114
GnomAD4 exome AF: 0.000131 AC: 191AN: 1455112Hom.: 1 Cov.: 30 AF XY: 0.000144 AC XY: 104AN XY: 722620
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74452
ClinVar
Submissions by phenotype
Koolen-de Vries syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at