16-3582636-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032444.4(SLX4):āc.5211G>Cā(p.Glu1737Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.5211G>C | p.Glu1737Asp | missense_variant | 15/15 | ENST00000294008.4 | NP_115820.2 | |
SLX4 | XM_024450471.2 | c.5211G>C | p.Glu1737Asp | missense_variant | 15/15 | XP_024306239.1 | ||
SLX4 | XM_011522715.4 | c.5208G>C | p.Glu1736Asp | missense_variant | 15/15 | XP_011521017.1 | ||
SLX4 | XM_047434801.1 | c.4209G>C | p.Glu1403Asp | missense_variant | 11/11 | XP_047290757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.5211G>C | p.Glu1737Asp | missense_variant | 15/15 | 5 | NM_032444.4 | ENSP00000294008.3 | ||
ENSG00000261938 | ENST00000573982.1 | n.199-500C>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249802Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135260
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461136Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 726932
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
Fanconi anemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 08, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 526393). This variant has not been reported in the literature in individuals affected with SLX4-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 1737 of the SLX4 protein (p.Glu1737Asp). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at