rs13083798

Variant names:

• chr3-52615732-A-G
• rs13083798
• NM_001405607.1:c.1864-276T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 44 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707071.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBRM1	NM_001405607.1	MANE Select	c.1864-276T>C		intron	N/A	NP_001392536.1
	PBRM1	NM_001405601.1		c.1864-276T>C		intron	N/A	NP_001392530.1
	PBRM1	NM_001405598.1		c.1846-276T>C		intron	N/A	NP_001392527.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBRM1	ENST00000707071.1	MANE Select	c.1864-276T>C		intron	N/A	ENSP00000516722.1
	PBRM1	ENST00000296302.11	TSL:1	c.1819-276T>C		intron	N/A	ENSP00000296302.7
	PBRM1	ENST00000409114.7	TSL:1	c.1864-276T>C		intron	N/A	ENSP00000386643.3

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

African (AFR) AF: 0.539 AC: 22332 AN: 41404

American (AMR) AF: 0.593 AC: 9055 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2347 AN: 5148

South Asian (SAS) AF: 0.301 AC: 1448 AN: 4818

European-Finnish (FIN) AF: 0.462 AC: 4865 AN: 10538

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33897 AN: 67920

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.509 Hom.: 27837

Bravo AF: 0.525

Asia WGS AF: 0.431 AC: 1499 AN: 3476

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.65
PhyloP100		0.14
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: rs13083798; hg19: chr3-52649748;