Variant chr3-52564343-T-C 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.3737-110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 820,578 control chromosomes in the GnomAD database, including 1,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.073 ( 958 hom., cov: 31)

Exomes 𝑓: 0.025 ( 608 hom. )

Consequence

PBRM1
ENST00000707071.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.900

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=-0.95).

BP6

Variant 3-52564343-T-C is Benign according to our data. Variant chr3-52564343-T-C is described in ClinVar as [Benign]. Clinvar id is 1282950.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 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.3737-110A>G		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1 linkuse as main transcript	n.3914-110A>G		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.3737-110A>G		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes

AF:

0.0724

AC:

11015

AN:

152100

Hom.:

952

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0406

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0380

Gnomad FIN

AF:

0.00584

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0203

Gnomad OTH

AF:

0.0598

GnomAD4 exome

AF:

0.0250

AC:

16726

AN:

668360

Hom.:

608

AF XY:

0.0248

AC XY:

8742

AN XY:

352248

show subpopulations

Gnomad4 AFR exome

AF:

0.224

Gnomad4 AMR exome

AF:

0.0268

Gnomad4 ASJ exome

AF:

0.0147

Gnomad4 EAS exome

AF:

0.000186

Gnomad4 SAS exome

AF:

0.0366

Gnomad4 FIN exome

AF:

0.00590

Gnomad4 NFE exome

AF:

0.0194

Gnomad4 OTH exome

AF:

0.0334

GnomAD4 genome

AF:

0.0726

AC:

11052

AN:

152218

Hom.:

958

Cov.:

AF XY:

0.0709

AC XY:

5276

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.0404

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.0382

Gnomad4 FIN

AF:

0.00584

Gnomad4 NFE

AF:

0.0203

Gnomad4 OTH

AF:

0.0596

Alfa

AF:

0.0531

Hom.:

Bravo

AF:

0.0824

Asia WGS

AF:

0.0280

AC:

100

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 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.42

DANN

Benign

0.60

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