16-51137019-AGGGGC-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_002968.3(SALL1):c.*88_*92del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000741 in 933,008 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0081 ( 1 hom., cov: 0)
Exomes 𝑓: 0.00032 ( 3 hom. )
Consequence
SALL1
NM_002968.3 3_prime_UTR
NM_002968.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.65
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 -16 ACMG points.
BP6
Variant 16-51137019-AGGGGC-A is Benign according to our data. Variant chr16-51137019-AGGGGC-A is described in ClinVar as [Likely_benign]. Clinvar id is 319593.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51137019-AGGGGC-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00814 (408/50116) while in subpopulation AFR AF= 0.0313 (388/12396). AF 95% confidence interval is 0.0287. There are 1 homozygotes in gnomad4. There are 200 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 408 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.*88_*92del | 3_prime_UTR_variant | 3/3 | ENST00000251020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.*88_*92del | 3_prime_UTR_variant | 3/3 | 1 | NM_002968.3 | P2 | ||
SALL1 | ENST00000440970.6 | c.*88_*92del | 3_prime_UTR_variant | 4/4 | 5 | P2 | |||
SALL1 | ENST00000685868.1 | c.*88_*92del | 3_prime_UTR_variant | 4/4 | P2 | ||||
SALL1 | ENST00000566102.1 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00813 AC: 407AN: 50078Hom.: 1 Cov.: 0
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GnomAD4 exome AF: 0.000321 AC: 283AN: 882892Hom.: 3 AF XY: 0.000302 AC XY: 137AN XY: 454038
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GnomAD4 genome AF: 0.00814 AC: 408AN: 50116Hom.: 1 Cov.: 0 AF XY: 0.00857 AC XY: 200AN XY: 23330
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 31, 2019 | - - |
Townes-Brocks syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at