rs11902616
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001164507.2(NEB):c.12018+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 1,540,414 control chromosomes in the GnomAD database, including 6,098 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 2289 hom., cov: 32)
Exomes 𝑓: 0.039 ( 3809 hom. )
Consequence
NEB
NM_001164507.2 intron
NM_001164507.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.494
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 2-151610487-C-T is Benign according to our data. Variant chr2-151610487-C-T is described in ClinVar as [Benign]. Clinvar id is 257726.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.12018+29G>A | intron_variant | ENST00000427231.7 | |||
NEB | NM_001164508.2 | c.12018+29G>A | intron_variant | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.12018+29G>A | intron_variant | 5 | NM_001164508.2 | P5 | |||
NEB | ENST00000427231.7 | c.12018+29G>A | intron_variant | 5 | NM_001164507.2 | A2 | |||
NEB | ENST00000409198.5 | c.11289+29G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17374AN: 151940Hom.: 2268 Cov.: 32
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GnomAD3 exomes AF: 0.0659 AC: 16298AN: 247142Hom.: 1469 AF XY: 0.0654 AC XY: 8762AN XY: 134012
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GnomAD4 exome AF: 0.0393 AC: 54577AN: 1388356Hom.: 3809 Cov.: 26 AF XY: 0.0414 AC XY: 28766AN XY: 694708
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GnomAD4 genome ? AF: 0.115 AC: 17460AN: 152058Hom.: 2289 Cov.: 32 AF XY: 0.114 AC XY: 8491AN XY: 74352
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Nemaline myopathy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Arthrogryposis multiplex congenita 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at