Variant chr6-3232126-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NR_147505.1(LOC100422781):n.724C>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 0.00502 in 702,452 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0047 ( 9 hom., cov: 33)

Exomes 𝑓: 0.0051 ( 19 hom. )

Consequence

LOC100422781
NR_147505.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0950

Variant links:

Genes affected

LOC100422781 (HGNC:):

LOC100422781 links:

PSMG4 (HGNC:21108): (proteasome assembly chaperone 4) Predicted to be involved in proteasome assembly. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

PSMG4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0028827786).

BP6

Variant 6-3232126-C-T is Benign according to our data. Variant chr6-3232126-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1676005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100422781	NR_147505.1 linkuse as main transcript	n.724C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein
PSMG4	ENST00000380306.8 linkuse as main transcript	c.38C>T	p.Pro13Leu	missense_variant	1/3	3	ENSP00000369661
PSMG4	ENST00000509933.1 linkuse as main transcript	c.38C>T	p.Pro13Leu	missense_variant, NMD_transcript_variant	1/3	2	ENSP00000422147
PSMG4	ENST00000416079.2 linkuse as main transcript	n.83+215C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00469

AC:

714

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0308

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00460

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00357

AC:

458

AN:

128312

Hom.:

AF XY:

0.00363

AC XY:

255

AN XY:

70274

show subpopulations

Gnomad AFR exome

AF:

0.000329

Gnomad AMR exome

AF:

0.000453

Gnomad ASJ exome

AF:

0.0129

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0282

Gnomad NFE exome

AF:

0.00363

Gnomad OTH exome

AF:

0.00400

GnomAD4 exome

AF:

0.00512

AC:

2815

AN:

550206

Hom.:

Cov.:

AF XY:

0.00488

AC XY:

1453

AN XY:

297854

show subpopulations

Gnomad4 AFR exome

AF:

0.000253

Gnomad4 AMR exome

AF:

0.000490

Gnomad4 ASJ exome

AF:

0.0131

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000319

Gnomad4 FIN exome

AF:

0.0264

Gnomad4 NFE exome

AF:

0.00479

Gnomad4 OTH exome

AF:

0.00435

GnomAD4 genome

AF:

0.00469

AC:

714

AN:

152246

Hom.:

Cov.:

AF XY:

0.00543

AC XY:

404

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.000361

Gnomad4 AMR

AF:

0.000393

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0308

Gnomad4 NFE

AF:

0.00460

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00861

Hom.:

Bravo

AF:

0.00203

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00104

AC:

ExAC

AF:

0.00238

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2023	ENSG00000288840: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.018

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.046

LIST_S2

Benign

0.34

MetaRNN

Benign

0.0029

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

PROVEAN

Benign

1.1

REVEL

Benign

0.020

Sift

Pathogenic

0.0

Vest4

0.081

MVP

0.040

ClinPred

0.020

GERP RS

1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over