dbSNP rs3813571: PSMA4:n.7G>T (chr15-78540450-G-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000559934.5(PSMA4):n.7G>T 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 152,410 control chromosomes in the GnomAD database, including 8,598 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 ( 8583 hom., cov: 33)

Exomes 𝑓: 0.38 ( 15 hom. )

Consequence

PSMA4
ENST00000559934.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77

Publications

23 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:

ENSG00000297264 (HGNC:):

ENSG00000297264 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

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 link	c.-113G>T		5_prime_UTR_variant	Exon 1 of 9	ENST00000044462.12	NP_002780.1	P25789-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMA4	ENST00000044462.12 link	c.-113G>T		5_prime_UTR_variant	Exon 1 of 9	1	NM_002789.6	ENSP00000044462.7		P25789-1

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47930

AN:

152114

Hom.:

8586

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.433

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.354

Gnomad EAS

AF:

0.166

Gnomad SAS

AF:

0.342

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.316

GnomAD4 exome

AF:

0.376

AC:

AN:

178

Hom.:

Cov.:

AF XY:

0.379

AC XY:

AN XY:

132

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.392

AC:

AN:

148

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.315

AC:

47939

AN:

152232

Hom.:

8583

Cov.:

AF XY:

0.312

AC XY:

23237

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.162

AC:

6736

AN:

41564

American (AMR)

AF:

0.249

AC:

3809

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.354

AC:

1228

AN:

3470

East Asian (EAS)

AF:

0.165

AC:

854

AN:

5174

South Asian (SAS)

AF:

0.341

AC:

1649

AN:

4830

European-Finnish (FIN)

AF:

0.370

AC:

3929

AN:

10612

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.421

AC:

28609

AN:

67968

Other (OTH)

AF:

0.317

AC:

671

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1629

3259

4888

6518

8147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.380

Hom.:

18878

Bravo

AF:

0.299

Asia WGS

AF:

0.271

AC:

941

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

1.8

PromoterAI

-0.32

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over