7-103352648-G-T

Variant summary

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

The NM_002803.4(PSMC2):c.71-1273G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00937 in 511,158 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0079 (4 hom., cov: 32)
  • Exomes 𝑓: 0.010 (38 hom.)
• Consequence: PSMC2 NM_002803.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.379

Genes affected

PSMC2 (HGNC:9548): (proteasome 26S subunit, ATPase 2) 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 one of the ATPase subunits, a member of the triple-A family of ATPases which have a chaperone-like activity. This subunit has been shown to interact with several of the basal transcription factors so, in addition to participation in proteasome functions, this subunit may participate in the regulation of transcription. This subunit may also compete with PSMC3 for binding to the HIV tat protein to regulate the interaction between the viral protein and the transcription complex. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 7-103352648-G-T is Benign according to our data. Variant chr7-103352648-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1194585.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 1197 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSMC2	NM_002803.4	c.71-1273G>T		intron_variant		ENST00000292644.5
PSMC2	NM_001204453.1	c.71-1273G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSMC2	ENST00000292644.5	c.71-1273G>T		intron_variant		1	NM_002803.4	P3

Frequencies

GnomAD3 genomes AF: 0.00788 AC: 1197 AN: 151978 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00813

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.00928

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.00478

GnomAD4 exome AF: 0.0100 AC: 3592 AN: 359062 Hom.: 38 AF XY: 0.00990 AC XY: 1905 AN XY: 192392

Gnomad4 AFR exome AF: 0.00149

Gnomad4 AMR exome AF: 0.00469

Gnomad4 ASJ exome AF: 0.00666

Gnomad4 EAS exome AF: 0.0000445

Gnomad4 SAS exome AF: 0.00708

Gnomad4 FIN exome AF: 0.00936

Gnomad4 NFE exome AF: 0.0127

Gnomad4 OTH exome AF: 0.0103

GnomAD4 genome AF: 0.00787 AC: 1197 AN: 152096 Hom.: 4 Cov.: 32 AF XY: 0.00749 AC XY: 557 AN XY: 74346

Gnomad4 AFR AF: 0.00234

Gnomad4 AMR AF: 0.00812

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.00928

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00204 Hom.: 0

Bravo AF: 0.00802

Asia WGS AF: 0.00173 AC: 7 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 23, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.51

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

Other links and lift over

dbSNP: rs73175850; hg19: chr7-102993095;