rs429608
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006929.5(SKIC2):c.1212-29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,607,370 control chromosomes in the GnomAD database, including 19,940 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.16 ( 2093 hom., cov: 31)
Exomes 𝑓: 0.15 ( 17847 hom. )
Consequence
SKIC2
NM_006929.5 intron
NM_006929.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.34
Genes affected
SKIC2 (HGNC:10898): (SKI2 subunit of superkiller complex) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a human homologue of yeast SKI2 and may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. This gene is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]
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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=-0.76).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKIC2 | NM_006929.5 | c.1212-29G>A | intron_variant | ENST00000375394.7 | |||
SKIC2 | XM_011514815.4 | c.1212-29G>A | intron_variant | ||||
SKIC2 | XM_047419259.1 | c.1212-29G>A | intron_variant | ||||
SKIC2 | XM_047419260.1 | c.1212-29G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKIC2 | ENST00000375394.7 | c.1212-29G>A | intron_variant | 1 | NM_006929.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24462AN: 151900Hom.: 2093 Cov.: 31
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GnomAD3 exomes AF: 0.143 AC: 35468AN: 248358Hom.: 2828 AF XY: 0.148 AC XY: 19884AN XY: 134760
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GnomAD4 exome AF: 0.153 AC: 222530AN: 1455352Hom.: 17847 Cov.: 31 AF XY: 0.154 AC XY: 111637AN XY: 724432
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GnomAD4 genome ? AF: 0.161 AC: 24489AN: 152018Hom.: 2093 Cov.: 31 AF XY: 0.159 AC XY: 11810AN XY: 74310
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | not provided | Department of Ophthalmology and Visual Sciences Kyoto University | - | - - |
Computational 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