chr16-51141744-C-CGCTGCTGCTGCT
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_002968.3(SALL1):c.466_477dupAGCAGCAGCAGC(p.Ser156_Ser159dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000197 in 1,580,028 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002968.3 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000113 AC: 17AN: 151000Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.000206 AC: 295AN: 1428918Hom.: 0 Cov.: 43 AF XY: 0.000293 AC XY: 208AN XY: 710692
GnomAD4 genome AF: 0.000113 AC: 17AN: 151110Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 73820
ClinVar
Submissions by phenotype
not provided Uncertain:2
Not observed at significant frequency in large population cohorts (gnomAD); In-frame insertion of 4 amino acids in a repetitive region with no known function; Has not been previously published as pathogenic or benign to our knowledge -
- -
not specified Benign:2
- -
- -
SALL1-related disorder Uncertain:1
The SALL1 c.466_477dup12 variant is predicted to result in an in-frame duplication (p.Ser156_Ser159dup). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Townes syndrome Uncertain:1
This variant, c.466_477dup, results in the insertion of 4 amino acid(s) of the SALL1 protein (p.Ser156_Ser159dup), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SALL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 591869). 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