rs12343516

Variant names:

• chr9-120841191-A-C
• rs12343516
• NM_005047.4:c.173+1546T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-120841191-A-C
• chr9-120841191-A-G
• chr9-120841191-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005047.4(PSMD5):​c.173+1546T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,162 control chromosomes in the GnomAD database, including 19,979 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 0.47 (19979 hom., cov: 33)
• Consequence: PSMD5 NM_005047.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 22 publications found

Genes affected

PSMD5 (HGNC:9563): (proteasome 26S subunit, non-ATPase 5) 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. This gene encodes a non-ATPase subunit of the 19S regulator base that functions as a chaperone protein during 26S proteasome assembly. [provided by RefSeq, Jul 2012]

CUTALP (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005047.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD5	NM_005047.4	MANE Select	c.173+1546T>G		intron	N/A	NP_005038.1	Q16401-1
	PSMD5	NM_001270427.2		c.173+1546T>G		intron	N/A	NP_001257356.1	Q16401-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD5	ENST00000210313.8	TSL:1 MANE Select	c.173+1546T>G		intron	N/A	ENSP00000210313.2	Q16401-1
	PSMD5	ENST00000373904.5	TSL:2	c.173+1546T>G		intron	N/A	ENSP00000363011.5	Q16401-2
	PSMD5	ENST00000963400.1		c.173+1546T>G		intron	N/A	ENSP00000633459.1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71606 AN: 152044 Hom.: 19968 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.471 AC: 71620 AN: 152162 Hom.: 19979 Cov.: 33 AF XY: 0.480 AC XY: 35680 AN XY: 74400

African (AFR) AF: 0.153 AC: 6368 AN: 41524

American (AMR) AF: 0.620 AC: 9486 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2458 AN: 5180

South Asian (SAS) AF: 0.736 AC: 3549 AN: 4824

European-Finnish (FIN) AF: 0.587 AC: 6209 AN: 10570

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39650 AN: 67990

Other (OTH) AF: 0.523 AC: 1105 AN: 2114

Alfa AF: 0.370 Hom.: 5058

Bravo AF: 0.457

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.39
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12343516; hg19: chr9-123603469;