rs200555425
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164507.2(NEB):c.367C>T(p.Arg123Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000657 in 1,613,068 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R123H) 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.367C>T | p.Arg123Cys | missense_variant | 6/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.367C>T | p.Arg123Cys | missense_variant | 6/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.367C>T | p.Arg123Cys | missense_variant | 6/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.367C>T | p.Arg123Cys | missense_variant | 6/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.367C>T | p.Arg123Cys | missense_variant | 6/150 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000125 AC: 31AN: 248746Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134952
GnomAD4 exome AF: 0.0000548 AC: 80AN: 1460864Hom.: 0 Cov.: 30 AF XY: 0.0000550 AC XY: 40AN XY: 726688
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74416
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.367C>T (p.R123C) alteration is located in exon 6 (coding exon 4) of the NEB gene. This alteration results from a C to T substitution at nucleotide position 367, causing the arginine (R) at amino acid position 123 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at