rs12956
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_012234.6(RYBP):c.*3065T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.221 in 232,850 control chromosomes in the GnomAD database, including 5,826 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 3819 hom., cov: 33)
Exomes 𝑓: 0.22 ( 2007 hom. )
Consequence
RYBP
NM_012234.6 3_prime_UTR
NM_012234.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.58
Genes affected
RYBP (HGNC:10480): (RING1 and YY1 binding protein) Predicted to enable DNA binding activity and transcription coregulator activity. Involved in several processes, including histone H2A monoubiquitination; negative regulation of proteasomal ubiquitin-dependent protein catabolic process; and positive regulation of transcription, DNA-templated. Located in nucleoplasm. Colocalizes with PcG protein complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYBP | NM_012234.6 | c.*3065T>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYBP | ENST00000477973.5 | c.*3065T>C | 3_prime_UTR_variant | 4/4 | 1 | P1 | |||
RYBP | ENST00000676660.1 | n.4797T>C | non_coding_transcript_exon_variant | 3/3 | |||||
RYBP | ENST00000677329.1 | n.3722T>C | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.222 AC: 33806AN: 152096Hom.: 3816 Cov.: 33
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GnomAD4 exome AF: 0.219 AC: 17627AN: 80636Hom.: 2007 Cov.: 0 AF XY: 0.216 AC XY: 8007AN XY: 37126
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GnomAD4 genome ? AF: 0.222 AC: 33820AN: 152214Hom.: 3819 Cov.: 33 AF XY: 0.223 AC XY: 16579AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
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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