rs10117466
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The variant allele was found at a frequency of 0.264 in 587,078 control chromosomes in the GnomAD database, including 23,215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5430 hom., cov: 32)
Exomes 𝑓: 0.27 ( 17785 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0310
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 9-134918015-G-T is Benign according to our data. Variant chr9-134918015-G-T is described in ClinVar as [Benign]. Clinvar id is 1252732.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.
Transcripts
RefSeq
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 37977AN: 151954Hom.: 5431 Cov.: 32
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GnomAD4 exome AF: 0.269 AC: 117109AN: 435006Hom.: 17785 AF XY: 0.266 AC XY: 61001AN XY: 229092
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GnomAD4 genome ? AF: 0.250 AC: 37968AN: 152072Hom.: 5430 Cov.: 32 AF XY: 0.247 AC XY: 18327AN XY: 74342
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 22, 2019 | This variant is associated with the following publications: (PMID: 22673311, 23209787) - |
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