rs13013209
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001164507.2(NEB):āc.7839G>Cā(p.Lys2613Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,613,728 control chromosomes in the GnomAD database, including 170,389 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K2613H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.7839G>C | p.Lys2613Asn | missense_variant | 57/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.7839G>C | p.Lys2613Asn | missense_variant | 57/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.7839G>C | p.Lys2613Asn | missense_variant | 57/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.7839G>C | p.Lys2613Asn | missense_variant | 57/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.7839G>C | p.Lys2613Asn | missense_variant | 57/150 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.351 AC: 53281AN: 151906Hom.: 11472 Cov.: 31
GnomAD3 exomes AF: 0.420 AC: 104730AN: 249250Hom.: 23355 AF XY: 0.424 AC XY: 57323AN XY: 135208
GnomAD4 exome AF: 0.459 AC: 671392AN: 1461704Hom.: 158922 Cov.: 118 AF XY: 0.458 AC XY: 332975AN XY: 727132
GnomAD4 genome ? AF: 0.350 AC: 53268AN: 152024Hom.: 11467 Cov.: 31 AF XY: 0.350 AC XY: 25995AN XY: 74284
ClinVar
Submissions by phenotype
not specified Benign:5
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 26, 2014 | p.Lys2613Asn in exon 57 of NEB: This variant is not expected to have clinical si gnificance because it has been identified in 47% (3979/8400) of European America n chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.ed u/EVS/; dbSNP rs13013209). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 23, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Nemaline myopathy 2 Benign:4
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 24, 2017 | Variant summary: The NEB c.7839G>C (p.Lys2613Asn) variant involves the alteration of a conserved nucleotide and 2/3 in silico tools (SNPs&GO and Mutation Taster not captured here due to low reliability index and p-value, respectively) predict a damaging outcome. This variant was found in 50096/120722 control chromosomes (11150 homozygotes) from ExAC at a frequency of 0.4149699, which is approximately 117 times the estimated maximal expected allele frequency of a pathogenic NEB variant (0.0035355), thus this variant is a common benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Therefore, the variant of interest has been classified as Benign. - |
Arthrogryposis multiplex congenita 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at