chr1-235810221-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS1
The NM_000081.4(LYST):c.597C>G(p.Asp199Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,614,052 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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. D199N) has been classified as Likely benign.
Frequency
Consequence
NM_000081.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYST | NM_000081.4 | c.597C>G | p.Asp199Glu | missense_variant | 5/53 | ENST00000389793.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYST | ENST00000389793.7 | c.597C>G | p.Asp199Glu | missense_variant | 5/53 | 5 | NM_000081.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00216 AC: 328AN: 152130Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000613 AC: 154AN: 251194Hom.: 1 AF XY: 0.000479 AC XY: 65AN XY: 135750
GnomAD4 exome AF: 0.000231 AC: 338AN: 1461804Hom.: 1 Cov.: 34 AF XY: 0.000190 AC XY: 138AN XY: 727210
GnomAD4 genome AF: 0.00219 AC: 334AN: 152248Hom.: 1 Cov.: 32 AF XY: 0.00212 AC XY: 158AN XY: 74432
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 13, 2020 | - - |
Chédiak-Higashi syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | LYST: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at