rs140784655
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001128227.3(GNE):c.1338C>T(p.Gly446=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,613,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G446G) has been classified as Likely benign.
Frequency
Consequence
NM_001128227.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNE | NM_001128227.3 | c.1338C>T | p.Gly446= | synonymous_variant | 7/12 | ENST00000396594.8 | |
GNE | NM_005476.7 | c.1245C>T | p.Gly415= | synonymous_variant | 7/12 | ENST00000642385.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNE | ENST00000396594.8 | c.1338C>T | p.Gly446= | synonymous_variant | 7/12 | 1 | NM_001128227.3 | ||
GNE | ENST00000642385.2 | c.1245C>T | p.Gly415= | synonymous_variant | 7/12 | NM_005476.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000552 AC: 84AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000290 AC: 73AN: 251446Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135900
GnomAD4 exome AF: 0.000144 AC: 210AN: 1461094Hom.: 0 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 726922
GnomAD4 genome ? AF: 0.000558 AC: 85AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | GNE: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 20, 2018 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 14, 2016 | - - |
Sialuria;C1853926:GNE myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at