chr5-94643279-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032290.4(SLF1):c.438G>T(p.Leu146Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000784 in 1,530,566 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. L146S) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.438G>T | p.Leu146Phe | missense_variant | 5/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.438G>T | p.Leu146Phe | missense_variant | 5/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000466957.1 | c.360+12536G>T | intron_variant, NMD_transcript_variant | 5 | |||||
SLF1 | ENST00000508130.5 | c.432-6175G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000701 AC: 1AN: 142672Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 75570
GnomAD4 exome AF: 0.00000725 AC: 10AN: 1378610Hom.: 0 Cov.: 29 AF XY: 0.00000588 AC XY: 4AN XY: 679932
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74196
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.438G>T (p.L146F) alteration is located in exon 5 (coding exon 4) of the SLF1 gene. This alteration results from a G to T substitution at nucleotide position 438, causing the leucine (L) at amino acid position 146 to be replaced by a phenylalanine (F). 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