rs12386601
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The variant allele was found at a frequency of 0.118 in 1,317,404 control chromosomes in the GnomAD database, including 9,581 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.12 ( 1163 hom., cov: 32)
Exomes 𝑓: 0.12 ( 8418 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.65
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 7-92528572-A-G is Benign according to our data. Variant chr7-92528572-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 256215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.121 AC: 18416AN: 151832Hom.: 1158 Cov.: 32
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GnomAD4 exome AF: 0.117 AC: 136454AN: 1165458Hom.: 8418 Cov.: 17 AF XY: 0.116 AC XY: 66043AN XY: 568846
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GnomAD4 genome ? AF: 0.121 AC: 18447AN: 151946Hom.: 1163 Cov.: 32 AF XY: 0.121 AC XY: 8993AN XY: 74286
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Zellweger spectrum disorders Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 18, 2021 | - - |
Peroxisome biogenesis disorder 1A (Zellweger) Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
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