rs1063128
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000081.4(LYST):c.1251A>G(p.Gln417Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,613,380 control chromosomes in the GnomAD database, including 124,443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000081.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.405 AC: 61533AN: 151790Hom.: 13165 Cov.: 31
GnomAD3 exomes AF: 0.345 AC: 86432AN: 250608Hom.: 16514 AF XY: 0.339 AC XY: 45958AN XY: 135486
GnomAD4 exome AF: 0.382 AC: 558950AN: 1461472Hom.: 111264 Cov.: 42 AF XY: 0.377 AC XY: 274165AN XY: 727034
GnomAD4 genome AF: 0.405 AC: 61595AN: 151908Hom.: 13179 Cov.: 31 AF XY: 0.398 AC XY: 29561AN XY: 74216
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is classified as Benign based on local population frequency. This variant was detected in 50% of patients studied by a panel of primary immunodeficiencies. Number of patients: 48. Only high quality variants are reported. -
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -
not provided Benign:2Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Chédiak-Higashi syndrome Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at