rs9713

Positions:

• chr2-161308497-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PSMD14	NM_005805.6	c.-245A>T		5_prime_UTR_premature_start_codon_gain_variant	1/12	ENST00000409682.8	NP_005796.1
PSMD14	NM_005805.6	c.-245A>T		5_prime_UTR_variant	1/12	ENST00000409682.8	NP_005796.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMD14	ENST00000409682	c.-245A>T		5_prime_UTR_premature_start_codon_gain_variant	1/12	1	NM_005805.6	ENSP00000386541.3
PSMD14	ENST00000409682	c.-245A>T		5_prime_UTR_variant	1/12	1	NM_005805.6	ENSP00000386541.3
PSMD14	ENST00000478123.5	n.37A>T		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102860 AN: 152050 Hom.: 35037 Cov.: 33

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: 60 AN: 76 Hom.: 23 Cov.: 0 AF XY: 0.828 AC XY: 48 AN XY: 58

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.803

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.676 AC: 102909 AN: 152168 Hom.: 35051 Cov.: 33 AF XY: 0.672 AC XY: 49976 AN XY: 74392

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.679

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
DANN	Benign	0.86
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0

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

LitVar

Other links and lift over

dbSNP: rs9713; hg19: chr2-162165008;