rs762410895
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PM1PM4PP3BS2
The NM_003036.4(SKI):βc.1445_1450delβ(p.Ala482_Glu483del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000548 in 1,460,300 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ). Synonymous variant affecting the same amino acid position (i.e. S480S) has been classified as Likely benign.
Frequency
Consequence
NM_003036.4 inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKI | NM_003036.4 | c.1445_1450del | p.Ala482_Glu483del | inframe_deletion | 4/7 | ENST00000378536.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKI | ENST00000378536.5 | c.1445_1450del | p.Ala482_Glu483del | inframe_deletion | 4/7 | 1 | NM_003036.4 | P1 | |
SKI | ENST00000507179.1 | n.428_433del | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246214Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133982
GnomAD4 exome AF: 0.0000548 AC: 80AN: 1460300Hom.: 0 AF XY: 0.0000454 AC XY: 33AN XY: 726452
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 03, 2015 | - - |
Shprintzen-Goldberg syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2022 | ClinVar contains an entry for this variant (Variation ID: 520744). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with SKI-related conditions. This variant is present in population databases (rs762410895, gnomAD 0.004%). This variant, c.1445_1450del, results in the deletion of 2 amino acid(s) of the SKI protein (p.Ala482_Glu483del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at