Variant 3-52550699-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000707071.1(PBRM1):c.4725+48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,582,072 control chromosomes in the GnomAD database, including 135,593 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 13402 hom., cov: 32)

Exomes 𝑓: 0.41 ( 122191 hom. )

Consequence

PBRM1
ENST00000707071.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.279

Variant links:

Genes affected

PBRM1 (HGNC:30064): (polybromo 1) This locus encodes a subunit of ATP-dependent chromatin-remodeling complexes. The encoded protein has been identified as in integral component of complexes necessary for ligand-dependent transcriptional activation by nuclear hormone receptors. Mutations at this locus have been associated with primary clear cell renal cell carcinoma. [provided by RefSeq, Feb 2012]

PBRM1 links:

UQCC5 (HGNC:37257): (ubiquinol-cytochrome c reductase complex assembly factor 5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

UQCC5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 3-52550699-A-G is Benign according to our data. Variant chr3-52550699-A-G is described in ClinVar as [Benign]. Clinvar id is 1178095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PBRM1	NM_001405607.1 linkuse as main transcript	c.4725+48T>C		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1 linkuse as main transcript	n.4869+48T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1 linkuse as main transcript	c.4725+48T>C		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63198

AN:

151970

Hom.:

13388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.425

GnomAD3 exomes

AF:

0.419

AC:

102049

AN:

243404

Hom.:

22082

AF XY:

0.408

AC XY:

53816

AN XY:

131760

show subpopulations

Gnomad AFR exome

AF:

0.389

Gnomad AMR exome

AF:

0.550

Gnomad ASJ exome

AF:

0.458

Gnomad EAS exome

AF:

0.425

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.411

Gnomad NFE exome

AF:

0.422

Gnomad OTH exome

AF:

0.411

GnomAD4 exome

AF:

0.410

AC:

586301

AN:

1429984

Hom.:

122191

Cov.:

AF XY:

0.405

AC XY:

288921

AN XY:

712700

show subpopulations

Gnomad4 AFR exome

AF:

0.394

Gnomad4 AMR exome

AF:

0.537

Gnomad4 ASJ exome

AF:

0.474

Gnomad4 EAS exome

AF:

0.477

Gnomad4 SAS exome

AF:

0.276

Gnomad4 FIN exome

AF:

0.408

Gnomad4 NFE exome

AF:

0.412

Gnomad4 OTH exome

AF:

0.401

GnomAD4 genome

AF:

0.416

AC:

63264

AN:

152088

Hom.:

13402

Cov.:

AF XY:

0.416

AC XY:

30953

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.279

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.431

Alfa

AF:

0.434

Hom.:

3652

Bravo

AF:

0.425

Asia WGS

AF:

0.384

AC:

1336

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 22, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.0

DANN

Benign

0.68

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

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