chr5-94643278-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032290.4(SLF1):āc.437T>Cā(p.Leu146Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000392 in 1,531,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L146F) has been classified as Uncertain significance.
Frequency
Consequence
NM_032290.4 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 | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.437T>C | p.Leu146Ser | missense_variant | 5/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.437T>C | p.Leu146Ser | missense_variant | 5/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000466957.1 | c.360+12535T>C | intron_variant, NMD_transcript_variant | 5 | |||||
SLF1 | ENST00000508130.5 | c.432-6176T>C | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000145 AC: 2AN: 1379578Hom.: 0 Cov.: 29 AF XY: 0.00000147 AC XY: 1AN XY: 680476
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2021 | The c.437T>C (p.L146S) alteration is located in exon 5 (coding exon 4) of the SLF1 gene. This alteration results from a T to C substitution at nucleotide position 437, causing the leucine (L) at amino acid position 146 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