chr14-100239240-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003403.5(YY1):c.-5C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,535,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
YY1
NM_003403.5 5_prime_UTR
NM_003403.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.315
Genes affected
YY1 (HGNC:12856): (YY1 transcription factor) YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YY1 | NM_003403.5 | c.-5C>T | 5_prime_UTR_variant | 1/5 | ENST00000262238.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YY1 | ENST00000262238.10 | c.-5C>T | 5_prime_UTR_variant | 1/5 | 1 | NM_003403.5 | P1 | ||
YY1 | ENST00000554371.1 | c.-5C>T | 5_prime_UTR_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000661 AC: 1AN: 151252Hom.: 0 Cov.: 28
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GnomAD4 exome AF: 0.0000166 AC: 23AN: 1384690Hom.: 0 Cov.: 32 AF XY: 0.0000161 AC XY: 11AN XY: 683894
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GnomAD4 genome ? AF: 0.00000661 AC: 1AN: 151252Hom.: 0 Cov.: 28 AF XY: 0.0000135 AC XY: 1AN XY: 73870
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Gabriele de Vries syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 05, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at