chr6-31961022-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006929.5(SKIC2):c.545-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 1,578,740 control chromosomes in the GnomAD database, including 415,008 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.78 ( 47010 hom., cov: 32)
Exomes 𝑓: 0.71 ( 367998 hom. )
Consequence
SKIC2
NM_006929.5 intron
NM_006929.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.140
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 6-31961022-T-C is Benign according to our data. Variant chr6-31961022-T-C is described in ClinVar as [Benign]. Clinvar id is 1165036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-31961022-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKIC2 | NM_006929.5 | c.545-19T>C | intron_variant | ENST00000375394.7 | |||
SKIC2 | XM_011514815.4 | c.545-19T>C | intron_variant | ||||
SKIC2 | XM_047419259.1 | c.545-19T>C | intron_variant | ||||
SKIC2 | XM_047419260.1 | c.545-19T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKIC2 | ENST00000375394.7 | c.545-19T>C | intron_variant | 1 | NM_006929.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.780 AC: 118626AN: 152064Hom.: 46954 Cov.: 32
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GnomAD3 exomes AF: 0.762 AC: 188838AN: 247734Hom.: 73006 AF XY: 0.771 AC XY: 103889AN XY: 134736
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GnomAD4 exome AF: 0.713 AC: 1017128AN: 1426558Hom.: 367998 Cov.: 28 AF XY: 0.721 AC XY: 512851AN XY: 711788
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GnomAD4 genome AF: 0.780 AC: 118742AN: 152182Hom.: 47010 Cov.: 32 AF XY: 0.783 AC XY: 58228AN XY: 74402
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Trichohepatoenteric syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at