dbSNP rs9713: PSMD14:c.-245A>T (chr2-161308497-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005805.6(PSMD14):c.-245A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,244 control chromosomes in the GnomAD database, including 35,074 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 0.68 ( 35051 hom., cov: 33)

Exomes 𝑓: 0.79 ( 23 hom. )

Consequence

PSMD14
NM_005805.6 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.352

Publications

9 publications found

Variant links:

Genes affected

PSMD14 (HGNC:16889): (proteasome 26S subunit, non-ATPase 14) This gene encodes a component of the 26S proteasome. The 26S proteasome is a large multiprotein complex that catalyzes the degradation of ubiquitinated intracellular proteins. The encoded protein is a component of the 19S regulatory cap complex of the 26S proteasome and mediates substrate deubiquitination. A pseudogene of this gene is also located on the long arm of chromosome 2. [provided by RefSeq, Feb 2012]

PSMD14 links:

PSMD14-DT (HGNC:56104): (PSMD14 divergent transcript)

PSMD14-DT 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=-0.74).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMD14	NM_005805.6 link	c.-245A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 12	ENST00000409682.8	NP_005796.1	O00487A0A140VKF2
PSMD14	NM_005805.6 link	c.-245A>T		5_prime_UTR_variant	Exon 1 of 12	ENST00000409682.8	NP_005796.1	O00487A0A140VKF2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMD14	ENST00000409682.8 link	c.-245A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 12	1	NM_005805.6	ENSP00000386541.3		O00487
PSMD14	ENST00000409682.8 link	c.-245A>T		5_prime_UTR_variant	Exon 1 of 12	1	NM_005805.6	ENSP00000386541.3		O00487

Frequencies

GnomAD3 genomes

AF:

0.676

AC:

102860

AN:

152050

Hom.:

35037

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.695

Gnomad AMR

AF:

0.723

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.618

Gnomad FIN

AF:

0.621

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.706

Gnomad OTH

AF:

0.685

GnomAD4 exome

AF:

0.789

AC:

AN:

Hom.:

Cov.:

AF XY:

0.828

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.803

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.676

AC:

102909

AN:

152168

Hom.:

35051

Cov.:

AF XY:

0.672

AC XY:

49976

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.648

AC:

26915

AN:

41522

American (AMR)

AF:

0.722

AC:

11040

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.702

AC:

2435

AN:

3470

East Asian (EAS)

AF:

0.524

AC:

2710

AN:

5170

South Asian (SAS)

AF:

0.618

AC:

2986

AN:

4830

European-Finnish (FIN)

AF:

0.621

AC:

6572

AN:

10588

Middle Eastern (MID)

AF:

0.711

AC:

209

AN:

294

European-Non Finnish (NFE)

AF:

0.706

AC:

47972

AN:

67982

Other (OTH)

AF:

0.679

AC:

1436

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1697

3395

5092

6790

8487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.507

Hom.:

999

Bravo

AF:

0.689

Asia WGS

AF:

0.527

AC:

1835

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

8.5

(source)

DANN

Benign

0.86

PhyloP100

0.35

PromoterAI

0.016

Neutral

(source)

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over