20-1154769-T-C

Position:

• chr20-1154769-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006814.5(PSMF1):​c.552-8361T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,058 control chromosomes in the GnomAD database, including 14,239 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 0.43 (14239 hom., cov: 32)
• Consequence: PSMF1 NM_006814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

PSMF1 (HGNC:9571): (proteasome inhibitor subunit 1) 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 protein that inhibits the activation of the proteasome by the 11S and 19S regulators. Alternative transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMF1	NM_006814.5	c.552-8361T>C		intron_variant		ENST00000335877.11	NP_006805.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMF1	ENST00000335877.11	c.552-8361T>C		intron_variant		1	NM_006814.5	ENSP00000338039	P1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64794 AN: 151940 Hom.: 14217 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.436

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.427 AC: 64856 AN: 152058 Hom.: 14239 Cov.: 32 AF XY: 0.430 AC XY: 31961 AN XY: 74328

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.435

Alfa AF: 0.407 Hom.: 2665

Bravo AF: 0.428

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.65

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: rs2300185; hg19: chr20-1135413;