rs79842542
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032444.4(SLX4):c.610C>T(p.Arg204Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 1,614,118 control chromosomes in the GnomAD database, including 3,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R204G) has been classified as Uncertain significance.
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.610C>T | p.Arg204Cys | missense_variant | 3/15 | ENST00000294008.4 | |
SLX4 | XM_024450471.2 | c.610C>T | p.Arg204Cys | missense_variant | 3/15 | ||
SLX4 | XM_011522715.4 | c.610C>T | p.Arg204Cys | missense_variant | 3/15 | ||
SLX4 | XR_007064923.1 | n.1259C>T | non_coding_transcript_exon_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.610C>T | p.Arg204Cys | missense_variant | 3/15 | 5 | NM_032444.4 | P1 | |
SLX4 | ENST00000466154.5 | n.905C>T | non_coding_transcript_exon_variant | 2/7 | 1 | ||||
SLX4 | ENST00000486524.1 | n.1238C>T | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
SLX4 | ENST00000697858.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0675 AC: 10274AN: 152126Hom.: 366 Cov.: 32
GnomAD3 exomes AF: 0.0630 AC: 15838AN: 251474Hom.: 582 AF XY: 0.0614 AC XY: 8349AN XY: 135914
GnomAD4 exome AF: 0.0633 AC: 92592AN: 1461874Hom.: 3153 Cov.: 33 AF XY: 0.0626 AC XY: 45515AN XY: 727236
GnomAD4 genome ? AF: 0.0675 AC: 10277AN: 152244Hom.: 366 Cov.: 32 AF XY: 0.0685 AC XY: 5097AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | curation | Leiden Open Variation Database | Aug 31, 2012 | Curator: Arleen D. Auerbach. Submitter to LOVD: Janine Bakker. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 19, 2016 | - - |
Fanconi anemia complementation group P Benign:2
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Fanconi anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at