rs369496789
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003036.4(SKI):c.1999-9C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000072 in 1,388,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
SKI
NM_003036.4 splice_polypyrimidine_tract, intron
NM_003036.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0007207
2
Clinical Significance
Conservation
PhyloP100: 2.58
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 1-2306568-C-G is Benign according to our data. Variant chr1-2306568-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 463403.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKI | NM_003036.4 | c.1999-9C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000378536.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKI | ENST00000378536.5 | c.1999-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003036.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.00000746 AC: 1AN: 133986Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 73054
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GnomAD4 exome AF: 7.20e-7 AC: 1AN: 1388678Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 685242
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
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Cov.:
33
Asia WGS
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3
AN:
3474
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Shprintzen-Goldberg syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2019 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at