16-29457656-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_024044.5(SLX1B):c.607C>T(p.Pro203Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024044.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLX1B | NM_024044.5 | c.607C>T | p.Pro203Ser | missense_variant | Exon 4 of 6 | NP_076949.1 | ||
SLX1B | NM_001400286.1 | c.601C>T | p.Pro201Ser | missense_variant | Exon 4 of 6 | NP_001387215.1 | ||
SLX1B | NM_178044.4 | c.265C>T | p.Pro89Ser | missense_variant | Exon 3 of 5 | NP_835145.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 13AN: 99128Hom.: 0 Cov.: 15 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000232 AC: 22AN: 947198Hom.: 0 Cov.: 14 AF XY: 0.0000235 AC XY: 11AN XY: 468134
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000131 AC: 13AN: 99128Hom.: 0 Cov.: 15 AF XY: 0.000149 AC XY: 7AN XY: 46848
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.607C>T (p.P203S) alteration is located in exon 4 (coding exon 4) of the SLX1B gene. This alteration results from a C to T substitution at nucleotide position 607, causing the proline (P) at amino acid position 203 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at