14-23042460-GC-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001099780.2(PSMB11):βc.237delβ(p.Ser80HisfsTer38) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00503 in 1,614,094 control chromosomes in the GnomAD database, including 47 homozygotes. Variant has been reported in ClinVar as Benign (β ).
Frequency
Genomes: π 0.0053 ( 6 hom., cov: 32)
Exomes π: 0.0050 ( 41 hom. )
Consequence
PSMB11
NM_001099780.2 frameshift
NM_001099780.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.53
Genes affected
PSMB11 (HGNC:31963): (proteasome subunit beta 11) Proteasomes generate peptides that are presented by major histocompatibility complex (MHC) I molecules to other cells of the immune system. Proteolysis is conducted by 20S proteasomes, complexes of 28 subunits arranged as a cylinder in 4 heteroheptameric rings: alpha-1 to -7, beta-1 to -7, beta-1 to -7, and alpha-1 to -7. The catalytic subunits are beta-1 (PSMB6; MIM 600307), beta-2 (PSMB7; MIM 604030), and beta-5 (PSMB5; MIM 600306). Three additional subunits, beta-1i (PSMB9; MIM 177045), beta-2i (PSMB10; MIM 176847), and beta-5i (PSMB8; MIM 177046), are induced by gamma-interferon (IFNG; MIM 147570) and are preferentially incorporated into proteasomes to make immunoproteasomes. PSMB11, or beta-5t, is a catalytic subunit expressed exclusively in cortical thymic epithelial cells (Murata et al., 2007 [PubMed 17540904]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 14-23042460-GC-G is Benign according to our data. Variant chr14-23042460-GC-G is described in ClinVar as [Benign]. Clinvar id is 710367.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMB11 | NM_001099780.2 | c.237del | p.Ser80HisfsTer38 | frameshift_variant | 1/1 | ENST00000408907.5 | NP_001093250.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMB11 | ENST00000408907.5 | c.237del | p.Ser80HisfsTer38 | frameshift_variant | 1/1 | NM_001099780.2 | ENSP00000386212 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00527 AC: 803AN: 152246Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00543 AC: 1355AN: 249370Hom.: 13 AF XY: 0.00572 AC XY: 774AN XY: 135328
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GnomAD4 exome AF: 0.00501 AC: 7320AN: 1461730Hom.: 41 Cov.: 32 AF XY: 0.00497 AC XY: 3615AN XY: 727178
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GnomAD4 genome AF: 0.00526 AC: 801AN: 152364Hom.: 6 Cov.: 32 AF XY: 0.00632 AC XY: 471AN XY: 74504
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 30, 2018 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at