rs202035863
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001164507.2(NEB):āc.863A>Gā(p.Lys288Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0028 in 1,610,250 control chromosomes in the GnomAD database, including 134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. K288K) has been classified as Likely benign.
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.863A>G | p.Lys288Arg | missense_variant | 11/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.863A>G | p.Lys288Arg | missense_variant | 11/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.863A>G | p.Lys288Arg | missense_variant | 11/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.863A>G | p.Lys288Arg | missense_variant | 11/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.863A>G | p.Lys288Arg | missense_variant | 11/150 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00169 AC: 257AN: 152196Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00580 AC: 1440AN: 248404Hom.: 35 AF XY: 0.00761 AC XY: 1026AN XY: 134764
GnomAD4 exome AF: 0.00291 AC: 4249AN: 1457936Hom.: 124 Cov.: 29 AF XY: 0.00423 AC XY: 3065AN XY: 725226
GnomAD4 genome ? AF: 0.00167 AC: 255AN: 152314Hom.: 10 Cov.: 32 AF XY: 0.00262 AC XY: 195AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 12, 2017 | 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 | Athena Diagnostics | Nov 18, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 27, 2016 | - - |
Nemaline myopathy 2 Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, 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 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 | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at