16-51141744-C-CGCCGCTGCTGCT
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS2
The NM_002968.3(SALL1):c.477_478insAGCAGCAGCGGC(p.Ser159_Gly160insSerSerSerGly) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000035 in 1,428,926 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: not found (cov: 31)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Consequence
SALL1
NM_002968.3 inframe_insertion
NM_002968.3 inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.34
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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| SALL1 | NM_002968.3 | c.477_478insAGCAGCAGCGGC | p.Ser159_Gly160insSerSerSerGly | inframe_insertion | 2/3 | ENST00000251020.9 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SALL1 | ENST00000251020.9 | c.477_478insAGCAGCAGCGGC | p.Ser159_Gly160insSerSerSerGly | inframe_insertion | 2/3 | 1 | NM_002968.3 | P2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000350 AC: 5AN: 1428926Hom.: 0 Cov.: 43 AF XY: 0.00000563 AC XY: 4AN XY: 710698
GnomAD4 exome
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43
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4
AN XY:
710698
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GnomAD4 genome
GnomAD4 genome
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31
Bravo
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ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at