16-3583367-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032444.4(SLX4):c.4883C>A(p.Thr1628Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,613,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.4883C>A | p.Thr1628Asn | missense_variant | Exon 14 of 15 | ENST00000294008.4 | NP_115820.2 | |
SLX4 | XM_024450471.2 | c.4883C>A | p.Thr1628Asn | missense_variant | Exon 14 of 15 | XP_024306239.1 | ||
SLX4 | XM_011522715.4 | c.4880C>A | p.Thr1627Asn | missense_variant | Exon 14 of 15 | XP_011521017.1 | ||
SLX4 | XM_047434801.1 | c.3881C>A | p.Thr1294Asn | missense_variant | Exon 10 of 11 | XP_047290757.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251140Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135732
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460918Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 726614
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74364
ClinVar
Submissions by phenotype
Fanconi anemia Uncertain:1
This sequence change replaces threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 1628 of the SLX4 protein (p.Thr1628Asn). 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 652842). 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 0.01%). -
Fanconi anemia complementation group P Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at