rs117443908
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003036.4(SKI):c.1734C>T(p.Ser578=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000272 in 1,570,768 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00052 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00025 ( 0 hom. )
Consequence
SKI
NM_003036.4 synonymous
NM_003036.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.18
Genes affected
SKI (HGNC:10896): (SKI proto-oncogene) This gene encodes the nuclear protooncogene protein homolog of avian sarcoma viral (v-ski) oncogene. It functions as a repressor of TGF-beta signaling, and may play a role in neural tube development and muscle differentiation. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 1-2304552-C-T is Benign according to our data. Variant chr1-2304552-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 415897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-4.18 with no splicing effect.
BS2
?
High AC in GnomAd4 at 79 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKI | NM_003036.4 | c.1734C>T | p.Ser578= | synonymous_variant | 5/7 | ENST00000378536.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKI | ENST00000378536.5 | c.1734C>T | p.Ser578= | synonymous_variant | 5/7 | 1 | NM_003036.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000519 AC: 79AN: 152254Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000652 AC: 118AN: 180844Hom.: 0 AF XY: 0.000587 AC XY: 57AN XY: 97022
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GnomAD4 exome AF: 0.000245 AC: 348AN: 1418396Hom.: 0 Cov.: 34 AF XY: 0.000238 AC XY: 167AN XY: 701852
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GnomAD4 genome ? AF: 0.000518 AC: 79AN: 152372Hom.: 1 Cov.: 33 AF XY: 0.000429 AC XY: 32AN XY: 74514
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Shprintzen-Goldberg syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 25, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 23, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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