16-51136405-CTT-C
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS1_Supporting
The NM_002968.3(SALL1):c.*705_*706del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0000197 in 152,298 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Consequence
SALL1
NM_002968.3 3_prime_UTR
NM_002968.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.08
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 -1 ACMG points.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000197 (3/152298) while in subpopulation EAS AF= 0.000578 (3/5190). AF 95% confidence interval is 0.000157. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.*705_*706del | 3_prime_UTR_variant | 3/3 | ENST00000251020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.*705_*706del | 3_prime_UTR_variant | 3/3 | 1 | NM_002968.3 | P2 | ||
SALL1 | ENST00000440970.6 | c.*705_*706del | 3_prime_UTR_variant | 4/4 | 5 | P2 | |||
SALL1 | ENST00000685868.1 | c.*705_*706del | 3_prime_UTR_variant | 4/4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74476
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Townes-Brocks syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at