rs786204996
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The variant allele was found at a frequency of 0.000477 in 113,114 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00048 ( 0 hom., 21 hem., cov: 24)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.92
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant X-18425418-G-T is Benign according to our data. Variant chrX-18425418-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 189604.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd4 at 21 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 55AN: 113064Hom.: 0 Cov.: 24 AF XY: 0.000625 AC XY: 22AN XY: 35200
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.000477 AC: 54AN: 113114Hom.: 0 Cov.: 24 AF XY: 0.000596 AC XY: 21AN XY: 35260
GnomAD4 genome
?
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113114
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24
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21
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35260
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ClinVar
Significance: Likely benign
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Atypical Rett syndrome Uncertain:1
Uncertain significance, no assertion criteria provided | curation | RettBASE | Mar 13, 2014 | No parental testing, unreported SNP - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | CDKL5: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at