rs78360334
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001353258.2(CYRIB):c.-190+7980A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00404 in 154,234 control chromosomes in the GnomAD database, including 27 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 0.0041 ( 27 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 0 hom. )
Consequence
CYRIB
NM_001353258.2 intron
NM_001353258.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0150
Genes affected
CYRIB (HGNC:25216): (CYFIP related Rac1 interactor B) Enables small GTPase binding activity. Involved in several processes, including cellular response to molecule of bacterial origin; negative regulation of small GTPase mediated signal transduction; and regulation of organelle organization. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
MIR5194 (HGNC:43498): (microRNA 5194) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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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 (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0879 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYRIB | NM_001353258.2 | c.-190+7980A>G | intron_variant | ENST00000694912.1 | |||
MIR5194 | NR_049826.1 | n.64A>G | non_coding_transcript_exon_variant | 1/1 | |||
LOC124902025 | XR_007061113.1 | n.665+2266A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYRIB | ENST00000694912.1 | c.-190+7980A>G | intron_variant | NM_001353258.2 | P4 | ||||
MIR5194 | ENST00000582634.1 | n.64A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00409 AC: 622AN: 152118Hom.: 26 Cov.: 32
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GnomAD3 exomes AF: 0.00877 AC: 1AN: 114Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 40
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GnomAD4 exome AF: 0.00100 AC: 2AN: 1998Hom.: 0 Cov.: 0 AF XY: 0.00199 AC XY: 2AN XY: 1004
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GnomAD4 genome ? AF: 0.00408 AC: 621AN: 152236Hom.: 27 Cov.: 32 AF XY: 0.00427 AC XY: 318AN XY: 74438
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at