14-23042460-GC-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001099780.2(PSMB11):​c.237del​(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: 𝑓 0.0053 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0050 ( 41 hom. )

Consequence

PSMB11
NM_001099780.2 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.53
Variant links:
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]

Genome browser will be placed here

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
PSMB11NM_001099780.2 linkuse as main transcriptc.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
PSMB11ENST00000408907.5 linkuse as main transcriptc.237del p.Ser80HisfsTer38 frameshift_variant 1/1 NM_001099780.2 ENSP00000386212 P1

Frequencies

GnomAD3 genomes
AF:
0.00527
AC:
803
AN:
152246
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000941
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00563
Gnomad ASJ
AF:
0.00490
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.0256
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00544
Gnomad OTH
AF:
0.00526
GnomAD3 exomes
AF:
0.00543
AC:
1355
AN:
249370
Hom.:
13
AF XY:
0.00572
AC XY:
774
AN XY:
135328
show subpopulations
Gnomad AFR exome
AF:
0.000709
Gnomad AMR exome
AF:
0.00377
Gnomad ASJ exome
AF:
0.00248
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00222
Gnomad FIN exome
AF:
0.0206
Gnomad NFE exome
AF:
0.00568
Gnomad OTH exome
AF:
0.00594
GnomAD4 exome
AF:
0.00501
AC:
7320
AN:
1461730
Hom.:
41
Cov.:
32
AF XY:
0.00497
AC XY:
3615
AN XY:
727178
show subpopulations
Gnomad4 AFR exome
AF:
0.000657
Gnomad4 AMR exome
AF:
0.00387
Gnomad4 ASJ exome
AF:
0.00260
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00234
Gnomad4 FIN exome
AF:
0.0199
Gnomad4 NFE exome
AF:
0.00495
Gnomad4 OTH exome
AF:
0.00474
GnomAD4 genome
AF:
0.00526
AC:
801
AN:
152364
Hom.:
6
Cov.:
32
AF XY:
0.00632
AC XY:
471
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.000938
Gnomad4 AMR
AF:
0.00562
Gnomad4 ASJ
AF:
0.00490
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.0256
Gnomad4 NFE
AF:
0.00542
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00148
Hom.:
0
Bravo
AF:
0.00377
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00474
EpiControl
AF:
0.00474

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 30, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs572934212; hg19: chr14-23511669; API