chr2-151512883-C-CAACA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001164507.2(NEB):c.23242-47_23242-46insTGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 1,328,656 control chromosomes in the GnomAD database, including 421 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.029 ( 86 hom., cov: 32)
Exomes 𝑓: 0.019 ( 335 hom. )
Consequence
NEB
NM_001164507.2 intron
NM_001164507.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.328
Genes affected
NEB (HGNC:7720): (nebulin) This gene encodes nebulin, a giant protein component of the cytoskeletal matrix that coexists with the thick and thin filaments within the sarcomeres of skeletal muscle. In most vertebrates, nebulin accounts for 3 to 4% of the total myofibrillar protein. The encoded protein contains approximately 30-amino acid long modules that can be classified into 7 types and other repeated modules. Protein isoform sizes vary from 600 to 800 kD due to alternative splicing that is tissue-, species-,and developmental stage-specific. Of the 183 exons in the nebulin gene, at least 43 are alternatively spliced, although exons 143 and 144 are not found in the same transcript. Of the several thousand transcript variants predicted for nebulin, the RefSeq Project has decided to create three representative RefSeq records. Mutations in this gene are associated with recessive nemaline myopathy. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 2-151512883-C-CAACA is Benign according to our data. Variant chr2-151512883-C-CAACA is described in ClinVar as [Benign]. Clinvar id is 257799.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0515 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.23242-47_23242-46insTGTT | intron_variant | ENST00000427231.7 | |||
NEB | NM_001164508.2 | c.23242-47_23242-46insTGTT | intron_variant | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.23242-47_23242-46insTGTT | intron_variant | 5 | NM_001164508.2 | P5 | |||
NEB | ENST00000427231.7 | c.23242-47_23242-46insTGTT | intron_variant | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0286 AC: 4358AN: 152154Hom.: 85 Cov.: 32
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GnomAD3 exomes AF: 0.0192 AC: 3740AN: 195180Hom.: 51 AF XY: 0.0183 AC XY: 1904AN XY: 104156
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GnomAD4 exome AF: 0.0195 AC: 22935AN: 1176384Hom.: 335 Cov.: 15 AF XY: 0.0189 AC XY: 11202AN XY: 594166
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GnomAD4 genome AF: 0.0287 AC: 4376AN: 152272Hom.: 86 Cov.: 32 AF XY: 0.0293 AC XY: 2178AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 07, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at