rs1965024
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002968.3(SALL1):c.2574C>T(p.Leu858=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 1,613,246 control chromosomes in the GnomAD database, including 338,355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.52 ( 23760 hom., cov: 33)
Exomes 𝑓: 0.65 ( 314595 hom. )
Consequence
SALL1
NM_002968.3 synonymous
NM_002968.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.39
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 16-51139648-G-A is Benign according to our data. Variant chr16-51139648-G-A is described in ClinVar as [Benign]. Clinvar id is 258866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51139648-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-2.39 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.2574C>T | p.Leu858= | synonymous_variant | 2/3 | ENST00000251020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.2574C>T | p.Leu858= | synonymous_variant | 2/3 | 1 | NM_002968.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.518 AC: 78718AN: 151988Hom.: 23755 Cov.: 33
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GnomAD3 exomes AF: 0.626 AC: 157353AN: 251370Hom.: 51414 AF XY: 0.638 AC XY: 86713AN XY: 135850
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GnomAD4 exome AF: 0.650 AC: 950250AN: 1461140Hom.: 314595 Cov.: 75 AF XY: 0.654 AC XY: 475254AN XY: 726798
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GnomAD4 genome ? AF: 0.518 AC: 78721AN: 152106Hom.: 23760 Cov.: 33 AF XY: 0.523 AC XY: 38875AN XY: 74364
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ClinVar
Significance: Benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Townes-Brocks syndrome 1 Benign:4
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Jun 21, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 24, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Townes syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at