chr15-78549947-C-T

Variant names:

• chr15-78549947-C-T
• rs1979906
• NM_002789.6:c.*1003C>T

Variant summary

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

The NM_002789.6(PSMA4):​c.*1003C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,698 control chromosomes in the GnomAD database, including 34,453 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 (34356 hom., cov: 32)
  • Exomes 𝑓: 0.56 (97 hom.)
• Consequence: PSMA4 NM_002789.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 22 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMA4	NM_002789.6	c.*1003C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000044462.12	NP_002780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMA4	ENST00000044462.12	c.*1003C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_002789.6	ENSP00000044462.7

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101088 AN: 151996 Hom.: 34312 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.674

GnomAD4 exome AF: 0.563 AC: 329 AN: 584 Hom.: 97 Cov.: 0 AF XY: 0.569 AC XY: 189 AN XY: 332

African (AFR) AF: 0.500 AC: 8 AN: 16

American (AMR) AF: 0.833 AC: 5 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 12 AN: 16

East Asian (EAS) AF: 0.906 AC: 29 AN: 32

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.609 AC: 56 AN: 92

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.515 AC: 204 AN: 396

Other (OTH) AF: 0.625 AC: 15 AN: 24

GnomAD4 genome AF: 0.665 AC: 101191 AN: 152114 Hom.: 34356 Cov.: 32 AF XY: 0.670 AC XY: 49802 AN XY: 74362

African (AFR) AF: 0.771 AC: 32007 AN: 41488

American (AMR) AF: 0.745 AC: 11394 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4332 AN: 5180

South Asian (SAS) AF: 0.669 AC: 3229 AN: 4828

European-Finnish (FIN) AF: 0.624 AC: 6589 AN: 10566

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

European-Non Finnish (NFE) AF: 0.577 AC: 39227 AN: 67976

Other (OTH) AF: 0.673 AC: 1422 AN: 2114

Alfa AF: 0.664 Hom.: 8694

Bravo AF: 0.678

Asia WGS AF: 0.731 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.22
PhyloP100		-0.86

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: rs1979906; hg19: chr15-78842289;