16-51137145-G-A
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_002968.3(SALL1):c.3942C>T(p.Phe1314=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0009 in 1,614,130 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00088 ( 18 hom. )
Consequence
SALL1
NM_002968.3 synonymous
NM_002968.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.518
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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 16-51137145-G-A is Benign according to our data. Variant chr16-51137145-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 319597.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.518 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00108 (165/152246) while in subpopulation SAS AF= 0.00976 (47/4816). AF 95% confidence interval is 0.00754. There are 1 homozygotes in gnomad4. There are 93 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 165 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.3942C>T | p.Phe1314= | synonymous_variant | 3/3 | ENST00000251020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.3942C>T | p.Phe1314= | synonymous_variant | 3/3 | 1 | NM_002968.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00110 AC: 167AN: 152128Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.00141 AC: 355AN: 251446Hom.: 6 AF XY: 0.00185 AC XY: 252AN XY: 135908
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GnomAD4 exome AF: 0.000881 AC: 1288AN: 1461884Hom.: 18 Cov.: 30 AF XY: 0.00113 AC XY: 820AN XY: 727244
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GnomAD4 genome AF: 0.00108 AC: 165AN: 152246Hom.: 1 Cov.: 31 AF XY: 0.00125 AC XY: 93AN XY: 74426
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | SALL1: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 31, 2019 | - - |
SALL1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 24, 2017 | - - |
Townes syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Townes-Brocks syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 30, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at