NM_032444.4:c.833G>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_032444.4(SLX4):c.833G>A(p.Arg278Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000305 in 1,614,180 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.833G>A | p.Arg278Gln | missense_variant | Exon 4 of 15 | ENST00000294008.4 | NP_115820.2 | |
SLX4 | XM_024450471.2 | c.833G>A | p.Arg278Gln | missense_variant | Exon 4 of 15 | XP_024306239.1 | ||
SLX4 | XM_011522715.4 | c.833G>A | p.Arg278Gln | missense_variant | Exon 4 of 15 | XP_011521017.1 | ||
SLX4 | XR_007064923.1 | n.1482G>A | non_coding_transcript_exon_variant | Exon 4 of 13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.833G>A | p.Arg278Gln | missense_variant | Exon 4 of 15 | 5 | NM_032444.4 | ENSP00000294008.3 | ||
SLX4 | ENST00000466154.5 | n.1128G>A | non_coding_transcript_exon_variant | Exon 3 of 7 | 1 | |||||
SLX4 | ENST00000486524.1 | n.1461G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 | |||||
SLX4 | ENST00000697858.1 | n.174G>A | non_coding_transcript_exon_variant | Exon 2 of 3 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000632 AC: 159AN: 251464Hom.: 1 AF XY: 0.000861 AC XY: 117AN XY: 135914
GnomAD4 exome AF: 0.000315 AC: 460AN: 1461852Hom.: 3 Cov.: 31 AF XY: 0.000452 AC XY: 329AN XY: 727216
GnomAD4 genome AF: 0.000210 AC: 32AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74486
ClinVar
Submissions by phenotype
Fanconi anemia complementation group P Uncertain:2Benign:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. Both variants have been previously reported in breast cancer patients [PMID 21805310, 22401137, 27153395, 23840564, 22383991] -
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). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
- -
Fanconi anemia Benign:2
- -
- -
not provided Benign:1
SLX4: PP3, BS1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at