rs375643423
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_032444.4(SLX4):āc.801G>Cā(p.Ala267=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A267A) has been classified as Likely benign.
Frequency
Consequence
NM_032444.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLX4 | NM_032444.4 | c.801G>C | p.Ala267= | synonymous_variant | 4/15 | ENST00000294008.4 | |
SLX4 | XM_024450471.2 | c.801G>C | p.Ala267= | synonymous_variant | 4/15 | ||
SLX4 | XM_011522715.4 | c.801G>C | p.Ala267= | synonymous_variant | 4/15 | ||
SLX4 | XR_007064923.1 | n.1450G>C | non_coding_transcript_exon_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLX4 | ENST00000294008.4 | c.801G>C | p.Ala267= | synonymous_variant | 4/15 | 5 | NM_032444.4 | P1 | |
SLX4 | ENST00000466154.5 | n.1096G>C | non_coding_transcript_exon_variant | 3/7 | 1 | ||||
SLX4 | ENST00000486524.1 | n.1429G>C | non_coding_transcript_exon_variant | 4/4 | 2 | ||||
SLX4 | ENST00000697858.1 | n.142G>C | non_coding_transcript_exon_variant | 2/3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251390Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461806Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727202
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at