19-42271848-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001386298.1(CIC):c.65C>T(p.Pro22Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00117 in 398,648 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 1 hom. )
Consequence
CIC
NM_001386298.1 missense
NM_001386298.1 missense
Scores
1
4
5
Clinical Significance
Conservation
PhyloP100: 4.25
Genes affected
CIC (HGNC:14214): (capicua transcriptional repressor) The protein encoded by this gene is an ortholog of the Drosophila melanogaster capicua gene, and is a member of the high mobility group (HMG)-box superfamily of transcriptional repressors. This protein contains a conserved HMG domain that is involved in DNA binding and nuclear localization, and a conserved C-terminus. Studies suggest that the N-terminal region of this protein interacts with Atxn1 (GeneID:6310), to form a transcription repressor complex, and in vitro studies suggest that polyglutamine-expansion of ATXN1 may alter the repressor activity of this complex. Mutations in this gene have been associated with olidogdendrogliomas (PMID:21817013). In addition, translocation events resulting in gene fusions of this gene with both DUX4 (GeneID:100288687) and FOXO4 (GeneID:4303) have been associated with round cell sarcomas. There are multiple pseudogenes of this gene found on chromosomes 1, 4, 6, 7, 16, 20, and the Y chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.13777766).
BP6
Variant 19-42271848-C-T is Benign according to our data. Variant chr19-42271848-C-T is described in ClinVar as [Benign]. Clinvar id is 2571046.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000998 (152/152236) while in subpopulation NFE AF= 0.0015 (102/68028). AF 95% confidence interval is 0.00126. There are 0 homozygotes in gnomad4. There are 75 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 152 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIC | NM_001386298.1 | c.65C>T | p.Pro22Leu | missense_variant | 2/21 | ENST00000681038.1 | NP_001373227.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CIC | ENST00000681038.1 | c.65C>T | p.Pro22Leu | missense_variant | 2/21 | NM_001386298.1 | ENSP00000505728.1 | |||
CIC | ENST00000572681.6 | c.65C>T | p.Pro22Leu | missense_variant | 2/21 | 5 | ENSP00000459719.1 |
Frequencies
GnomAD3 genomes AF: 0.000998 AC: 152AN: 152236Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00128 AC: 315AN: 246412Hom.: 1 Cov.: 0 AF XY: 0.00115 AC XY: 143AN XY: 124872
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GnomAD4 genome AF: 0.000998 AC: 152AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.00101 AC XY: 75AN XY: 74370
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CIC-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 05, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | CIC: BS1, BS2 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
Sift4G
Uncertain
D;D
Vest4
MVP
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at