rs760435859
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032444.4(SLX4):c.5404G>T(p.Asp1802Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.5404G>T | p.Asp1802Tyr | missense_variant | 15/15 | ENST00000294008.4 | NP_115820.2 | |
SLX4 | XM_024450471.2 | c.5404G>T | p.Asp1802Tyr | missense_variant | 15/15 | XP_024306239.1 | ||
SLX4 | XM_011522715.4 | c.5401G>T | p.Asp1801Tyr | missense_variant | 15/15 | XP_011521017.1 | ||
SLX4 | XM_047434801.1 | c.4402G>T | p.Asp1468Tyr | missense_variant | 11/11 | XP_047290757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.5404G>T | p.Asp1802Tyr | missense_variant | 15/15 | 5 | NM_032444.4 | ENSP00000294008 | P1 | |
ENST00000573982.1 | n.199-693C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250146Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135402
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461606Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727118
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at