chr2-151506941-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 3P and 3B. PM2PP3BP4_ModerateBP6
The NM_001164507.2(NEB):c.23524C>T(p.Arg7842Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000969 in 1,610,100 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. R7842H) 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.23524C>T | p.Arg7842Cys | missense_variant | 163/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.23524C>T | p.Arg7842Cys | missense_variant | 163/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.23524C>T | p.Arg7842Cys | missense_variant | 163/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.23524C>T | p.Arg7842Cys | missense_variant | 163/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000454 AC: 69AN: 152058Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000145 AC: 36AN: 248508Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134836
GnomAD4 exome AF: 0.0000597 AC: 87AN: 1457924Hom.: 0 Cov.: 29 AF XY: 0.0000455 AC XY: 33AN XY: 725432
GnomAD4 genome AF: 0.000453 AC: 69AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74418
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 01, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 28, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27535533) - |
NEB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 02, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at