rs139125293
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001164507.2(NEB):c.1829G>A(p.Gly610Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G610R) has been classified as Uncertain significance.
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.1829G>A | p.Gly610Glu | missense_variant | 20/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.1829G>A | p.Gly610Glu | missense_variant | 20/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.1829G>A | p.Gly610Glu | missense_variant | 20/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.1829G>A | p.Gly610Glu | missense_variant | 20/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000489048.1 | n.728G>A | non_coding_transcript_exon_variant | 8/12 | 1 | ||||
NEB | ENST00000409198.5 | c.1829G>A | p.Gly610Glu | missense_variant | 20/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249228Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135202
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727138
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74450
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 02, 2021 | This sequence change replaces glycine with glutamic acid at codon 610 of the NEB protein (p.Gly610Glu). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and glutamic acid. This variant is present in population databases (rs139125293, ExAC 0.05%). This variant has not been reported in the literature in individuals affected with NEB-related conditions. ClinVar contains an entry for this variant (Variation ID: 521170). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). 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. - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at