dbSNP rs559422: PSMD13:n.1268A>C (chr11-248181-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000527047.5(PSMD13):n.1268A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0642 in 153,046 control chromosomes in the GnomAD database, including 413 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.064 ( 413 hom., cov: 32)

Exomes 𝑓: 0.057 ( 0 hom. )

Consequence

PSMD13
ENST00000527047.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.771

Publications

7 publications found

Variant links:

Genes affected

PSMD13 (HGNC:9558): (proteasome 26S subunit, non-ATPase 13) The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. Two transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

PSMD13 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PSMD13	NM_002817.4 link	c.569-595A>C	intron_variant	Intron 7 of 12	ENST00000532097.6	NP_002808.3	Q9UNM6-1
PSMD13	NM_175932.3 link	c.575-595A>C	intron_variant	Intron 5 of 10		NP_787128.2	Q9UNM6-2
PSMD13	XM_011520235.4 link	c.569-595A>C	intron_variant	Intron 7 of 10		XP_011518537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMD13	ENST00000532097.6 link	c.569-595A>C		intron_variant	Intron 7 of 12	1	NM_002817.4	ENSP00000436186.1		Q9UNM6-1

Frequencies

GnomAD3 genomes

AF:

0.0641

AC:

9743

AN:

151984

Hom.:

409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0270

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0741

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.0118

Gnomad SAS

AF:

0.0516

Gnomad FIN

AF:

0.0824

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0847

Gnomad OTH

AF:

0.0607

GnomAD4 exome

AF:

0.0572

AC:

AN:

944

Hom.:

Cov.:

AF XY:

0.0587

AC XY:

AN XY:

494

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.0221

AC:

AN:

136

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0303

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0657

AC:

AN:

700

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0642

AC:

9766

AN:

152102

Hom.:

413

Cov.:

AF XY:

0.0637

AC XY:

4732

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.0275

AC:

1141

AN:

41488

American (AMR)

AF:

0.0739

AC:

1129

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

402

AN:

3464

East Asian (EAS)

AF:

0.0118

AC:

AN:

5178

South Asian (SAS)

AF:

0.0516

AC:

249

AN:

4824

European-Finnish (FIN)

AF:

0.0824

AC:

871

AN:

10564

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0847

AC:

5756

AN:

67994

Other (OTH)

AF:

0.0624

AC:

132

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

483

966

1450

1933

2416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0762

Hom.:

549

Bravo

AF:

0.0631

Asia WGS

AF:

0.0640

AC:

222

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.30

(source)

DANN

Benign

0.73

PhyloP100

-0.77

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over