rs397718862
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001164507.2(NEB):c.822+27_822+28insGCC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 38670 hom., cov: 0)
Exomes 𝑓: 0.79 ( 405711 hom. )
Consequence
NEB
NM_001164507.2 intron
NM_001164507.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.499
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 2-151717388-A-AGGC is Benign according to our data. Variant chr2-151717388-A-AGGC is described in ClinVar as [Benign]. Clinvar id is 257832.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.822+27_822+28insGCC | intron_variant | ENST00000427231.7 | |||
NEB | NM_001164508.2 | c.822+27_822+28insGCC | intron_variant | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.822+27_822+28insGCC | intron_variant | 5 | NM_001164508.2 | P5 | |||
NEB | ENST00000427231.7 | c.822+27_822+28insGCC | intron_variant | 5 | NM_001164507.2 | A2 | |||
NEB | ENST00000409198.5 | c.822+27_822+28insGCC | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.681 AC: 103287AN: 151722Hom.: 38664 Cov.: 0
GnomAD3 genomes
AF:
AC:
103287
AN:
151722
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.754 AC: 183267AN: 243122Hom.: 72025 AF XY: 0.756 AC XY: 99574AN XY: 131766
GnomAD3 exomes
AF:
AC:
183267
AN:
243122
Hom.:
AF XY:
AC XY:
99574
AN XY:
131766
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.790 AC: 1004056AN: 1271144Hom.: 405711 Cov.: 20 AF XY: 0.788 AC XY: 505748AN XY: 641958
GnomAD4 exome
AF:
AC:
1004056
AN:
1271144
Hom.:
Cov.:
20
AF XY:
AC XY:
505748
AN XY:
641958
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.680 AC: 103305AN: 151842Hom.: 38670 Cov.: 0 AF XY: 0.684 AC XY: 50735AN XY: 74226
GnomAD4 genome
AF:
AC:
103305
AN:
151842
Hom.:
Cov.:
0
AF XY:
AC XY:
50735
AN XY:
74226
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
1733
AN:
3478
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 | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at