chr6-30555147-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005275.5(GNL1):c.284G>A(p.Arg95Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,460,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005275.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNL1 | NM_005275.5 | c.284G>A | p.Arg95Lys | missense_variant | 3/12 | ENST00000376621.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNL1 | ENST00000376621.8 | c.284G>A | p.Arg95Lys | missense_variant | 3/12 | 1 | NM_005275.5 | P1 | |
GNL1 | ENST00000433809.1 | c.278G>A | p.Arg93Lys | missense_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000324 AC: 8AN: 247118Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134610
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1460766Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6AN XY: 726694
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.284G>A (p.R95K) alteration is located in exon 3 (coding exon 3) of the GNL1 gene. This alteration results from a G to A substitution at nucleotide position 284, causing the arginine (R) at amino acid position 95 to be replaced by a lysine (K). 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