chr2-161342482-T-C

Variant names:

• chr2-161342482-T-C
• rs10197817
• NM_005805.6:c.48+23609T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005805.6(PSMD14):​c.48+23609T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,994 control chromosomes in the GnomAD database, including 34,686 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 (34686 hom., cov: 32)
• Consequence: PSMD14 NM_005805.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005805.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14	NM_005805.6	MANE Select	c.48+23609T>C		intron	N/A	NP_005796.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14	ENST00000409682.8	TSL:1 MANE Select	c.48+23609T>C		intron	N/A	ENSP00000386541.3
	PSMD14	ENST00000961542.1		c.48+23609T>C		intron	N/A	ENSP00000631601.1
	PSMD14	ENST00000899669.1		c.48+23609T>C		intron	N/A	ENSP00000569728.1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102241 AN: 151876 Hom.: 34669 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.683

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.673 AC: 102296 AN: 151994 Hom.: 34686 Cov.: 32 AF XY: 0.669 AC XY: 49676 AN XY: 74308

African (AFR) AF: 0.636 AC: 26344 AN: 41444

American (AMR) AF: 0.722 AC: 11034 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2435 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2725 AN: 5178

South Asian (SAS) AF: 0.618 AC: 2982 AN: 4822

European-Finnish (FIN) AF: 0.619 AC: 6520 AN: 10526

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47985 AN: 67966

Other (OTH) AF: 0.677 AC: 1428 AN: 2108

Alfa AF: 0.700 Hom.: 41822

Bravo AF: 0.686

Asia WGS AF: 0.528 AC: 1834 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.59
PhyloP100		0.26
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10197817; hg19: chr2-162198993;