2-216482771-CAGA-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_014140.4(SMARCAL1):c.2662_2664delAAG(p.Lys888del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000041 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_014140.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCAL1 | NM_014140.4 | c.2662_2664delAAG | p.Lys888del | conservative_inframe_deletion | Exon 18 of 18 | ENST00000357276.9 | NP_054859.2 | |
SMARCAL1 | NM_001127207.2 | c.2662_2664delAAG | p.Lys888del | conservative_inframe_deletion | Exon 18 of 18 | NP_001120679.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251304Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135814
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461878Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727240
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Schimke immuno-osseous dysplasia Uncertain:2
- -
This variant, c.2662_2664del, results in the deletion of 1 amino acid(s) of the SMARCAL1 protein (p.Lys888del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SMARCAL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1513538). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at