chr16-3608868-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032444.4(SLX4):c.97G>C(p.Asp33His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D33E) has been classified as Uncertain significance.
Frequency
Consequence
NM_032444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.97G>C | p.Asp33His | missense_variant | 2/15 | ENST00000294008.4 | |
SLX4 | XM_024450471.2 | c.97G>C | p.Asp33His | missense_variant | 2/15 | ||
SLX4 | XM_011522715.4 | c.97G>C | p.Asp33His | missense_variant | 2/15 | ||
SLX4 | XR_007064923.1 | n.746G>C | non_coding_transcript_exon_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.97G>C | p.Asp33His | missense_variant | 2/15 | 5 | NM_032444.4 | P1 | |
SLX4 | ENST00000466154.5 | n.392G>C | non_coding_transcript_exon_variant | 1/7 | 1 | ||||
SLX4 | ENST00000486524.1 | n.725G>C | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
SLX4 | ENST00000697859.1 | n.719G>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at