10-100916896-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018121.4(SLF2):c.511C>T(p.Pro171Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P171L) has been classified as Uncertain significance.
Frequency
Consequence
NM_018121.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLF2 | ENST00000238961.9 | c.511C>T | p.Pro171Ser | missense_variant | Exon 3 of 20 | 1 | NM_018121.4 | ENSP00000238961.3 | ||
SLF2 | ENST00000370269.3 | c.511C>T | p.Pro171Ser | missense_variant | Exon 3 of 19 | 1 | ENSP00000359292.3 | |||
SLF2 | ENST00000370271.7 | c.511C>T | p.Pro171Ser | missense_variant | Exon 3 of 6 | 1 | ENSP00000359294.3 | |||
SLF2 | ENST00000649226.1 | n.511C>T | non_coding_transcript_exon_variant | Exon 3 of 21 | ENSP00000496951.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251270Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135828
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.511C>T (p.P171S) alteration is located in exon 3 (coding exon 3) of the SLF2 gene. This alteration results from a C to T substitution at nucleotide position 511, causing the proline (P) at amino acid position 171 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