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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559934.5. 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.-113G>T	5_prime_UTR	Exon 1 of 9	NP_002780.1
PSMA4	NM_001102667.2		c.-37G>T	5_prime_UTR	Exon 1 of 9	NP_001096137.1
PSMA4	NM_001330675.2		c.-113G>T	5_prime_UTR	Exon 1 of 9	NP_001317604.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PSMA4	ENST00000559934.5	TSL:1	n.7G>T	non_coding_transcript_exon	Exon 1 of 6
PSMA4	ENST00000044462.12	TSL:1 MANE Select	c.-113G>T	5_prime_UTR	Exon 1 of 9	ENSP00000044462.7
PSMA4	ENST00000413382.6	TSL:1	c.-163G>T	5_prime_UTR	Exon 1 of 8	ENSP00000402118.2

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over