rs151130915
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_000081.4(LYST):c.3217A>G(p.Ile1073Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000081.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000171 AC: 43AN: 250956Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135626
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461740Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727178
GnomAD4 genome AF: 0.000552 AC: 84AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function -
Chédiak-Higashi syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at