chr5-94643343-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032290.4(SLF1):c.502G>T(p.Ala168Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000278 in 1,544,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. A168V) 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.502G>T | p.Ala168Ser | missense_variant | 5/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.502G>T | p.Ala168Ser | missense_variant | 5/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000466957.1 | c.360+12600G>T | intron_variant, NMD_transcript_variant | 5 | |||||
SLF1 | ENST00000508130.5 | c.432-6111G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000654 AC: 10AN: 152984Hom.: 0 AF XY: 0.000111 AC XY: 9AN XY: 81026
GnomAD4 exome AF: 0.0000294 AC: 41AN: 1392788Hom.: 0 Cov.: 29 AF XY: 0.0000379 AC XY: 26AN XY: 686854
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.502G>T (p.A168S) 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 502, causing the alanine (A) at amino acid position 168 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