rs3828057
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005060.4(RORC):c.1396-68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 1,539,496 control chromosomes in the GnomAD database, including 140,099 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.36 ( 10796 hom., cov: 32)
Exomes 𝑓: 0.43 ( 129303 hom. )
Consequence
RORC
NM_005060.4 intron
NM_005060.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.458
Genes affected
RORC (HGNC:10260): (RAR related orphan receptor C) The protein encoded by this gene is a DNA-binding transcription factor and is a member of the NR1 subfamily of nuclear hormone receptors. The specific functions of this protein are not known; however, studies of a similar gene in mice have shown that this gene may be essential for lymphoid organogenesis and may play an important regulatory role in thymopoiesis. In addition, studies in mice suggest that the protein encoded by this gene may inhibit the expression of Fas ligand and IL2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 1-151807701-C-T is Benign according to our data. Variant chr1-151807701-C-T is described in ClinVar as [Benign]. Clinvar id is 2628172.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RORC | NM_005060.4 | c.1396-68G>A | intron_variant | ENST00000318247.7 | |||
RORC | NM_001001523.2 | c.1333-68G>A | intron_variant | ||||
RORC | XM_006711484.5 | c.1558-68G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RORC | ENST00000318247.7 | c.1396-68G>A | intron_variant | 1 | NM_005060.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.362 AC: 54952AN: 151992Hom.: 10796 Cov.: 32
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GnomAD4 exome AF: 0.425 AC: 590296AN: 1387388Hom.: 129303 AF XY: 0.425 AC XY: 292460AN XY: 688468
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GnomAD4 genome ? AF: 0.361 AC: 54955AN: 152108Hom.: 10796 Cov.: 32 AF XY: 0.354 AC XY: 26344AN XY: 74366
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 51% of patients studied by a panel of primary immunodeficiencies. Number of patients: 49. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at