rs138615800
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032444.4(SLX4):c.710G>A(p.Arg237Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00523 in 1,614,176 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.710G>A | p.Arg237Gln | missense_variant | 3/15 | ENST00000294008.4 | NP_115820.2 | |
SLX4 | XM_024450471.2 | c.710G>A | p.Arg237Gln | missense_variant | 3/15 | XP_024306239.1 | ||
SLX4 | XM_011522715.4 | c.710G>A | p.Arg237Gln | missense_variant | 3/15 | XP_011521017.1 | ||
SLX4 | XR_007064923.1 | n.1359G>A | non_coding_transcript_exon_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.710G>A | p.Arg237Gln | missense_variant | 3/15 | 5 | NM_032444.4 | ENSP00000294008 | P1 | |
SLX4 | ENST00000466154.5 | n.1005G>A | non_coding_transcript_exon_variant | 2/7 | 1 | |||||
SLX4 | ENST00000486524.1 | n.1338G>A | non_coding_transcript_exon_variant | 3/4 | 2 | |||||
SLX4 | ENST00000697858.1 | n.51G>A | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes AF: 0.00797 AC: 1213AN: 152170Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00474 AC: 1189AN: 251012Hom.: 8 AF XY: 0.00436 AC XY: 591AN XY: 135702
GnomAD4 exome AF: 0.00495 AC: 7237AN: 1461890Hom.: 27 Cov.: 33 AF XY: 0.00473 AC XY: 3438AN XY: 727246
GnomAD4 genome AF: 0.00797 AC: 1213AN: 152286Hom.: 5 Cov.: 32 AF XY: 0.00790 AC XY: 588AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:5
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 | Genetic Services Laboratory, University of Chicago | Dec 07, 2016 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Fanconi anemia complementation group P Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 05, 2017 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Fanconi anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at