rs73721294
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014390.4(SND1):c.2110+381C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00698 in 539,510 control chromosomes in the GnomAD database, including 128 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 0.019 ( 103 hom., cov: 33)
Exomes 𝑓: 0.0024 ( 25 hom. )
Consequence
SND1
NM_014390.4 intron
NM_014390.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.184
Genes affected
SND1 (HGNC:30646): (staphylococcal nuclease and tudor domain containing 1) This gene encodes a transcriptional co-activator that interacts with the acidic domain of Epstein-Barr virus nuclear antigen 2 (EBNA 2), a transcriptional activator that is required for B-lymphocyte transformation. Other transcription factors that interact with this protein are signal transducers and activators of transcription, STATs. This protein is also thought to be essential for normal cell growth. A similar protein in mammals and other organisms is a component of the RNA-induced silencing complex (RISC). [provided by RefSeq, Jul 2016]
MIR593 (HGNC:32849): (microRNA 593) 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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.2110+381C>T | intron_variant | ENST00000354725.8 | |||
MIR593 | NR_030324.1 | n.22C>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.2110+381C>T | intron_variant | 1 | NM_014390.4 | P1 | |||
MIR593 | ENST00000384856.1 | n.22C>T | mature_miRNA_variant | 1/1 | |||||
SND1 | ENST00000486037.1 | c.568+381C>T | intron_variant | 3 | |||||
SND1 | ENST00000470463.1 | n.494+381C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0187 AC: 2839AN: 152182Hom.: 101 Cov.: 33
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GnomAD3 exomes AF: 0.00500 AC: 1256AN: 251058Hom.: 37 AF XY: 0.00366 AC XY: 497AN XY: 135904
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GnomAD4 exome AF: 0.00237 AC: 919AN: 387210Hom.: 25 Cov.: 0 AF XY: 0.00184 AC XY: 405AN XY: 220170
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GnomAD4 genome ? AF: 0.0187 AC: 2846AN: 152300Hom.: 103 Cov.: 33 AF XY: 0.0177 AC XY: 1321AN XY: 74480
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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