rs80186343
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032444.4(SLX4):c.2013+137G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 930,750 control chromosomes in the GnomAD database, including 1,934 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.072 ( 410 hom., cov: 32)
Exomes 𝑓: 0.059 ( 1524 hom. )
Consequence
SLX4
NM_032444.4 intron
NM_032444.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.34
Genes affected
SLX4 (HGNC:23845): (SLX4 structure-specific endonuclease subunit) This gene encodes a protein that functions as an assembly component of multiple structure-specific endonucleases. These endonuclease complexes are required for repair of specific types of DNA lesions and critical for cellular responses to replication fork failure. Mutations in this gene were found in patients with Fanconi anemia. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 16-3595468-C-G is Benign according to our data. Variant chr16-3595468-C-G is described in ClinVar as [Benign]. Clinvar id is 929586.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-3595468-C-G is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0868 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.2013+137G>C | intron_variant | ENST00000294008.4 | NP_115820.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.2013+137G>C | intron_variant | 5 | NM_032444.4 | ENSP00000294008.3 |
Frequencies
GnomAD3 genomes AF: 0.0721 AC: 10969AN: 152128Hom.: 407 Cov.: 32
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GnomAD4 exome AF: 0.0594 AC: 46205AN: 778504Hom.: 1524 AF XY: 0.0584 AC XY: 23695AN XY: 405790
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GnomAD4 genome AF: 0.0721 AC: 10983AN: 152246Hom.: 410 Cov.: 32 AF XY: 0.0726 AC XY: 5403AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | curation | Leiden Open Variation Database | Aug 31, 2012 | Curator: Arleen D. Auerbach. Submitter to LOVD: Janine Bakker. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at