rs568814745
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001164507.2(NEB):c.10118G>A(p.Arg3373Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,613,904 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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. R3373W) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.10118G>A | p.Arg3373Gln | missense_variant | 69/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.10118G>A | p.Arg3373Gln | missense_variant | 69/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.10118G>A | p.Arg3373Gln | missense_variant | 69/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.10118G>A | p.Arg3373Gln | missense_variant | 69/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.9389G>A | p.Arg3130Gln | missense_variant | 66/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000165 AC: 41AN: 248896Hom.: 0 AF XY: 0.000230 AC XY: 31AN XY: 135040
GnomAD4 exome AF: 0.000185 AC: 270AN: 1461656Hom.: 1 Cov.: 32 AF XY: 0.000231 AC XY: 168AN XY: 727104
GnomAD4 genome AF: 0.000151 AC: 23AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74426
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 17, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 31, 2017 | The R3373Q variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R3373Q variant is observed in 7/66,704 (0.01%) alleles from individuals of European background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Most reported pathogenic variants in the NEB gene are truncating/loss-of-function. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. However, this variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. - |
Nemaline myopathy 2 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 03, 2022 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 3373 of the NEB protein (p.Arg3373Gln). This variant is present in population databases (rs568814745, gnomAD 0.07%). 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: 451633). 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"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. | Jan 17, 2020 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.9389G>A (p.R3130Q) alteration is located in exon 66 (coding exon 64) of the NEB gene. This alteration results from a G to A substitution at nucleotide position 9389, causing the arginine (R) at amino acid position 3130 to be replaced by a glutamine (Q). 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