rs1160316709
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001040167.2(LFNG):c.643G>A(p.Ala215Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000131 in 152,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040167.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LFNG | NM_001040167.2 | c.643G>A | p.Ala215Thr | missense_variant | Exon 4 of 8 | ENST00000222725.10 | NP_001035257.1 | |
LFNG | NM_001040168.2 | c.643G>A | p.Ala215Thr | missense_variant | Exon 4 of 8 | NP_001035258.1 | ||
LFNG | NM_001166355.2 | c.430G>A | p.Ala144Thr | missense_variant | Exon 5 of 9 | NP_001159827.1 | ||
LFNG | NM_002304.3 | c.256G>A | p.Ala86Thr | missense_variant | Exon 5 of 9 | NP_002295.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152252Hom.: 0 Cov.: 34
GnomAD4 exome Cov.: 34
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152252Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74392
ClinVar
Submissions by phenotype
Spondylocostal dysostosis 3, autosomal recessive Uncertain:1
In summary, this variant has uncertain impact on LFNG function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with a LFNG-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with threonine at codon 215 of the LFNG protein (p.Ala215Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at