rs201780688
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005275.5(GNL1):c.830G>T(p.Arg277Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000893 in 1,613,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. R277P) has been classified as Uncertain significance.
Frequency
Consequence
NM_005275.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNL1 | NM_005275.5 | c.830G>T | p.Arg277Leu | missense_variant | Exon 7 of 12 | ENST00000376621.8 | NP_005266.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNL1 | ENST00000376621.8 | c.830G>T | p.Arg277Leu | missense_variant | Exon 7 of 12 | 1 | NM_005275.5 | ENSP00000365806.3 | ||
GNL1 | ENST00000433809.1 | c.*202G>T | downstream_gene_variant | 2 | ENSP00000404728.1 | |||||
GNL1 | ENST00000487166.1 | n.-38G>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251328Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135804
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461102Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 726914
GnomAD4 genome AF: 0.000105 AC: 16AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.830G>T (p.R277L) alteration is located in exon 7 (coding exon 7) of the GNL1 gene. This alteration results from a G to T substitution at nucleotide position 830, causing the arginine (R) at amino acid position 277 to be replaced by a leucine (L). 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