NM_002816.5:c.1073T>C

Variant names:

• chr17-67344616-A-G
• rs2230680
• NM_002816.5:c.1073T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_002816.5(PSMD12):​c.1073T>C​(p.Val358Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000419 in 1,608,002 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

• Frequency:
  • Genomes: 𝑓 0.0022 (2 hom., cov: 33)
  • Exomes 𝑓: 0.00023 (4 hom.)
• Consequence: PSMD12 NM_002816.5 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.89

Genes affected

PSMD12 (HGNC:9557): (proteasome 26S subunit, non-ATPase 12) 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. A pseudogene has been identified on chromosome 3. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0120461285).
• BP6: Variant 17-67344616-A-G is Benign according to our data. Variant chr17-67344616-A-G is described in ClinVar as [Benign]. Clinvar id is 2648116.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 336 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMD12	NM_002816.5	c.1073T>C	p.Val358Ala	missense_variant	Exon 9 of 11	ENST00000356126.8	NP_002807.1
PSMD12	NM_174871.4	c.1013T>C	p.Val338Ala	missense_variant	Exon 8 of 10		NP_777360.1
PSMD12	NM_001316341.2	c.896T>C	p.Val299Ala	missense_variant	Exon 11 of 13		NP_001303270.1
PSMD12	XM_047436440.1	c.*154T>C		downstream_gene_variant			XP_047292396.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMD12	ENST00000356126.8	c.1073T>C	p.Val358Ala	missense_variant	Exon 9 of 11	1	NM_002816.5	ENSP00000348442.3
PSMD12	ENST00000584008.5	n.*1228T>C		non_coding_transcript_exon_variant	Exon 11 of 13	1		ENSP00000462525.1
PSMD12	ENST00000584008.5	n.*1228T>C		3_prime_UTR_variant	Exon 11 of 13	1		ENSP00000462525.1
PSMD12	ENST00000357146.4	c.1013T>C	p.Val338Ala	missense_variant	Exon 8 of 10	2		ENSP00000349667.4

Frequencies

GnomAD3 genomes AF: 0.00220 AC: 335 AN: 152182 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.00787

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.000605 AC: 151 AN: 249582 Hom.: 3 AF XY: 0.000489 AC XY: 66 AN XY: 135026

Gnomad AFR exome AF: 0.00839

Gnomad AMR exome AF: 0.000324

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000657

GnomAD4 exome AF: 0.000232 AC: 338 AN: 1455702 Hom.: 4 Cov.: 31 AF XY: 0.000211 AC XY: 153 AN XY: 723880

Gnomad4 AFR exome AF: 0.00859

Gnomad4 AMR exome AF: 0.000363

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000541

Gnomad4 OTH exome AF: 0.000499

GnomAD4 genome AF: 0.00221 AC: 336 AN: 152300 Hom.: 2 Cov.: 33 AF XY: 0.00218 AC XY: 162 AN XY: 74470

Gnomad4 AFR AF: 0.00787

Gnomad4 AMR AF: 0.000392

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00175 Hom.: 0

Bravo AF: 0.00275

ESP6500AA AF: 0.00772 AC: 34

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000659 AC: 80

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PSMD12: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Uncertain	0.010
CADD	Pathogenic	26
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.27	T;.
Eigen	Pathogenic	0.85
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.77	T;T
M_CAP	Benign	0.076	D
MetaRNN	Benign	0.012	T;T
MetaSVM	Uncertain	-0.28	T
MutationAssessor	Pathogenic	3.1	M;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-3.5	D;D
REVEL	Uncertain	0.46
Sift	Uncertain	0.014	D;D
Sift4G	Pathogenic	0.0010	D;D
Polyphen		0.99	D;.
Vest4		0.47
MVP		0.46
MPC		1.7
ClinPred		0.066	T
GERP RS		5.6
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.6
Varity_R		0.54
gMVP		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

Other links and lift over

dbSNP: rs2230680; hg19: chr17-65340732;