16-51141744-CGCTGCTGCTGCTGCTGCT-CGCT
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002968.3(SALL1):c.463_477delAGCAGCAGCAGCAGC(p.Ser155_Ser159del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,579,926 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
SALL1
NM_002968.3 conservative_inframe_deletion
NM_002968.3 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.79
Genes affected
SALL1 (HGNC:10524): (spalt like transcription factor 1) The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 25 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151000Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000175 AC: 25AN: 1428926Hom.: 0 AF XY: 0.0000197 AC XY: 14AN XY: 710698
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151000Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73702
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at