rs894871556
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001008537.3(NEXMIF):c.2363T>G(p.Leu788Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000893 in 112,044 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001008537.3 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 |
---|---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.2363T>G | p.Leu788Arg | missense_variant | Exon 3 of 4 | 1 | NM_001008537.3 | ENSP00000055682.5 | ||
NEXMIF | ENST00000616200.2 | c.2363T>G | p.Leu788Arg | missense_variant | Exon 3 of 5 | 1 | ENSP00000480284.1 | |||
NEXMIF | ENST00000642681.2 | c.2363T>G | p.Leu788Arg | missense_variant | Exon 3 of 3 | ENSP00000495800.1 |
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 112044Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34194
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000893 AC: 1AN: 112044Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34194
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces leucine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 788 of the NEXMIF protein (p.Leu788Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NEXMIF-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at