chr2-151494232-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001164507.2(NEB):c.24508G>A(p.Gly8170Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G8170E) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.24508G>A | p.Gly8170Arg | missense_variant | 174/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.24508G>A | p.Gly8170Arg | missense_variant | 174/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.24508G>A | p.Gly8170Arg | missense_variant | 174/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.24508G>A | p.Gly8170Arg | missense_variant | 174/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 09, 2018 | This variant has not been reported in the literature in individuals with an NEB-related disease. ClinVar contains an entry for this variant (Variation ID: 465582). This sequence change replaces glycine with arginine at codon 8205 of the NEB protein (p.Gly8205Arg). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and arginine. In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: ":Probably Damaging"; Align-GVGD: "Class C0"). This variant is not present in population databases (ExAC no frequency). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at