chr15-78540246-T-C

Variant names:

• chr15-78540246-T-C
• rs3813572
• ENST00000746668.1:n.100A>G

Variant summary

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

The ENST00000746668.1(ENSG00000297264):​n.100A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,114 control chromosomes in the GnomAD database, including 8,574 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 0.31 (8574 hom., cov: 32)
• Consequence: ENSG00000297264 ENST00000746668.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 14 publications found

Genes affected

ENSG00000297264 (HGNC:):

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMA4	NM_002789.6	c.-317T>C		upstream_gene_variant		ENST00000044462.12	NP_002780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMA4	ENST00000044462.12	c.-317T>C		upstream_gene_variant		1	NM_002789.6	ENSP00000044462.7

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47898 AN: 151996 Hom.: 8577 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.315 AC: 47907 AN: 152114 Hom.: 8574 Cov.: 32 AF XY: 0.312 AC XY: 23213 AN XY: 74362

African (AFR) AF: 0.162 AC: 6729 AN: 41516

American (AMR) AF: 0.249 AC: 3815 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3462

East Asian (EAS) AF: 0.165 AC: 855 AN: 5168

South Asian (SAS) AF: 0.340 AC: 1639 AN: 4814

European-Finnish (FIN) AF: 0.372 AC: 3933 AN: 10584

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28591 AN: 67960

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.377 Hom.: 6376

Bravo AF: 0.299

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.4
DANN	Benign	0.74
PhyloP100		-0.45
PromoterAI		-0.0059	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3813572; hg19: chr15-78832588;