rs12901682

Variant names:

• chr15-78540881-A-C
• rs12901682
• ENST00000559934.5:n.438A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-78540881-A-C
• chr15-78540881-A-T

Variant summary

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

The ENST00000559934.5(PSMA4):​n.438A>C 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 0.94 in 152,228 control chromosomes in the GnomAD database, including 67,664 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 0.94 (67625 hom., cov: 30)
  • Exomes 𝑓: 0.98 (39 hom.)
• Consequence: PSMA4 ENST00000559934.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 16 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]

ENSG00000297479 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMA4	NM_002789.6	c.-24+342A>C		intron_variant	Intron 1 of 8	ENST00000044462.12	NP_002780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMA4	ENST00000044462.12	c.-24+342A>C		intron_variant	Intron 1 of 8	1	NM_002789.6	ENSP00000044462.7

Frequencies

GnomAD3 genomes AF: 0.940 AC: 142943 AN: 152028 Hom.: 67579 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.947

GnomAD4 exome AF: 0.976 AC: 80 AN: 82 Hom.: 39 Cov.: 0 AF XY: 0.955 AC XY: 42 AN XY: 44

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 10 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 52 AN: 52

Other (OTH) AF: 0.875 AC: 7 AN: 8

GnomAD4 genome AF: 0.940 AC: 143045 AN: 152146 Hom.: 67625 Cov.: 30 AF XY: 0.942 AC XY: 70039 AN XY: 74378

African (AFR) AF: 0.831 AC: 34435 AN: 41456

American (AMR) AF: 0.976 AC: 14920 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4522 AN: 5160

South Asian (SAS) AF: 0.980 AC: 4720 AN: 4814

European-Finnish (FIN) AF: 0.984 AC: 10449 AN: 10616

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.991 AC: 67424 AN: 68022

Other (OTH) AF: 0.948 AC: 2002 AN: 2112

Alfa AF: 0.973 Hom.: 280176

Bravo AF: 0.933

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.67
PhyloP100		-0.066
PromoterAI		-0.070	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs12901682; hg19: chr15-78833223;