chr16-51136183-CAAG-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_002968.3(SALL1):c.*926_*928del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00244 in 152,700 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0046 ( 0 hom. )
Consequence
SALL1
NM_002968.3 3_prime_UTR
NM_002968.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.30
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 Benign. Variant got -9 ACMG points.
BP6
?
Variant 16-51136183-CAAG-C is Benign according to our data. Variant chr16-51136183-CAAG-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 319579.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00244 (371/152266) while in subpopulation NFE AF= 0.0039 (265/68012). AF 95% confidence interval is 0.00351. There are 0 homozygotes in gnomad4. There are 180 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 371 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.*926_*928del | 3_prime_UTR_variant | 3/3 | ENST00000251020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.*926_*928del | 3_prime_UTR_variant | 3/3 | 1 | NM_002968.3 | P2 | ||
SALL1 | ENST00000440970.6 | c.*926_*928del | 3_prime_UTR_variant | 4/4 | 5 | P2 | |||
SALL1 | ENST00000685868.1 | c.*926_*928del | 3_prime_UTR_variant | 4/4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00244 AC: 371AN: 152148Hom.: 0 Cov.: 33
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GnomAD4 genome ? AF: 0.00244 AC: 371AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.00242 AC XY: 180AN XY: 74440
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
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 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | SALL1: BS1 - |
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