rs45459896
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002968.3(SALL1):āc.2544A>Gā(p.Gln848=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 1,614,222 control chromosomes in the GnomAD database, including 191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0090 ( 12 hom., cov: 32)
Exomes š: 0.014 ( 179 hom. )
Consequence
SALL1
NM_002968.3 synonymous
NM_002968.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0320
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=-0.72).
BP6
?
Variant 16-51139678-T-C is Benign according to our data. Variant chr16-51139678-T-C is described in ClinVar as [Benign]. Clinvar id is 258865.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51139678-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.032 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00901 (1372/152342) while in subpopulation NFE AF= 0.0148 (1008/68036). AF 95% confidence interval is 0.0141. There are 12 homozygotes in gnomad4. There are 644 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1372 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.2544A>G | p.Gln848= | synonymous_variant | 2/3 | ENST00000251020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.2544A>G | p.Gln848= | synonymous_variant | 2/3 | 1 | NM_002968.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00903 AC: 1374AN: 152224Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00913 AC: 2296AN: 251476Hom.: 18 AF XY: 0.00918 AC XY: 1247AN XY: 135908
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GnomAD4 exome AF: 0.0140 AC: 20524AN: 1461880Hom.: 179 Cov.: 56 AF XY: 0.0138 AC XY: 10020AN XY: 727242
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GnomAD4 genome ? AF: 0.00901 AC: 1372AN: 152342Hom.: 12 Cov.: 32 AF XY: 0.00865 AC XY: 644AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 12, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | SALL1: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:1
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 16, 2024 | - - |
Computational scores
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Name
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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