15-78552014-A-G

Variant names:

• chr15-78552014-A-G
• rs880395
• NM_002789.6:c.*3070A>G

Variant summary

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

The NM_002789.6(PSMA4):​c.*3070A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,142 control chromosomes in the GnomAD database, including 34,582 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 0.67 (34582 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PSMA4 NM_002789.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 21 publications found

Genes affected

PSMA4 (HGNC:9533): (proteasome 20S subunit alpha 4) This gene encodes a core alpha subunit of the 20S proteosome, which is a highly ordered ring-shaped structure composed of four rings of 28 non-identical subunits. Proteasomes cleave peptides in an ATP- and ubiquitin-dependent manner. [provided by RefSeq, Aug 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002789.6. 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
	PSMA4	NM_002789.6	MANE Select	c.*3070A>G		3_prime_UTR	Exon 9 of 9	NP_002780.1	P25789-1
	PSMA4	NM_001330676.2		c.*3070A>G		3_prime_UTR	Exon 9 of 9	NP_001317605.1	P25789-1
	PSMA4	NM_001330675.2		c.*3070A>G		3_prime_UTR	Exon 9 of 9	NP_001317604.1	H0YN18

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMA4	ENST00000044462.12	TSL:1 MANE Select	c.*3070A>G		3_prime_UTR	Exon 9 of 9	ENSP00000044462.7	P25789-1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101378 AN: 152020 Hom.: 34538 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.676

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.667 AC: 101481 AN: 152138 Hom.: 34582 Cov.: 33 AF XY: 0.671 AC XY: 49929 AN XY: 74380

African (AFR) AF: 0.773 AC: 32085 AN: 41520

American (AMR) AF: 0.760 AC: 11613 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4321 AN: 5170

South Asian (SAS) AF: 0.669 AC: 3226 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6587 AN: 10574

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39238 AN: 67986

Other (OTH) AF: 0.675 AC: 1424 AN: 2110

Alfa AF: 0.642 Hom.: 4738

Bravo AF: 0.682

Asia WGS AF: 0.732 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		0.29

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

Other links and lift over

dbSNP: rs880395; hg19: chr15-78844356;