rs13083798

chr3-52615732-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000707071.1(PBRM1):c.1864-276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,874 control chromosomes in the GnomAD database, including 20,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.51 (20087 hom., cov: 31)
• Consequence: PBRM1 ENST00000707071.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.142

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 3-52615732-A-G is Benign according to our data. Variant chr3-52615732-A-G is described in ClinVar as [Benign]. Clinvar id is 1232523.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PBRM1	NM_001405607.1	c.1864-276T>C		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1	n.2041-276T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1	c.1864-276T>C		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77438 AN: 151754 Hom.: 20067 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.510 AC: 77511 AN: 151874 Hom.: 20087 Cov.: 31 AF XY: 0.507 AC XY: 37604 AN XY: 74224

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.523

Alfa AF: 0.518 Hom.: 3797

Bravo AF: 0.525

Asia WGS AF: 0.431 AC: 1499 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.2
Dann	Benign	0.65

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: rs13083798; hg19: chr3-52649748;