dbSNP rs1979905: PSMA4:c.*1088A>C (chr15-78550032-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002789.6(PSMA4):c.*1088A>C 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 152,140 control chromosomes in the GnomAD database, including 34,375 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 ( 34364 hom., cov: 33)

Exomes 𝑓: 0.65 ( 11 hom. )

Consequence

PSMA4
NM_002789.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.237

Publications

17 publications found

Variant links:

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]

PSMA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 = 0.816 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PSMA4	NM_002789.6	MANE Select	c.*1088A>C	3_prime_UTR	Exon 9 of 9	NP_002780.1
PSMA4	NM_001330676.2		c.*1088A>C	3_prime_UTR	Exon 9 of 9	NP_001317605.1
PSMA4	NM_001330675.2		c.*1088A>C	3_prime_UTR	Exon 9 of 9	NP_001317604.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMA4	ENST00000044462.12	TSL:1 MANE Select	c.*1088A>C		3_prime_UTR	Exon 9 of 9	ENSP00000044462.7

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

101080

AN:

151976

Hom.:

34320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.772

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:

0.623

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.674

GnomAD4 exome

AF:

0.652

AC:

AN:

Hom.:

Cov.:

AF XY:

0.618

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.875

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.567

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.665

AC:

101183

AN:

152094

Hom.:

34364

Cov.:

AF XY:

0.670

AC XY:

49804

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.772

AC:

32008

AN:

41474

American (AMR)

AF:

0.745

AC:

11402

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.646

AC:

2242

AN:

3472

East Asian (EAS)

AF:

0.837

AC:

4330

AN:

5176

South Asian (SAS)

AF:

0.669

AC:

3226

AN:

4824

European-Finnish (FIN)

AF:

0.623

AC:

6583

AN:

10562

Middle Eastern (MID)

AF:

0.786

AC:

231

AN:

294

European-Non Finnish (NFE)

AF:

0.577

AC:

39226

AN:

67976

Other (OTH)

AF:

0.672

AC:

1417

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1681

3362

5042

6723

8404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.634

Hom.:

6109

Bravo

AF:

0.678

Asia WGS

AF:

0.731

AC:

2542

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

1.6

(source)

DANN

Benign

0.73

PhyloP100

-0.24

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over