chr3-52587570-C-CT

Position:

• chr3-52587570-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000707071.1(PBRM1):​c.3011-61_3011-60insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 716,016 control chromosomes in the GnomAD database, including 807 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.074 (806 hom., cov: 29)
  • Exomes 𝑓: 0.15 (1 hom.)
• Consequence: PBRM1 ENST00000707071.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.167

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 -10 ACMG points.

• BP6: Variant 3-52587570-C-CT is Benign according to our data. Variant chr3-52587570-C-CT is described in ClinVar as [Benign]. Clinvar id is 1262624.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PBRM1	NM_001405607.1	c.3011-61_3011-60insA		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1	n.3188-61_3188-60insA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1	c.3011-61_3011-60insA		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 9708 AN: 131332 Hom.: 806 Cov.: 29

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00352

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0185

Gnomad EAS AF: 0.00432

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.00909

Gnomad MID AF: 0.0468

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.0623

GnomAD4 exome AF: 0.155 AC: 90529 AN: 584702 Hom.: 1 AF XY: 0.156 AC XY: 46906 AN XY: 301190

Gnomad4 AFR exome AF: 0.234

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.152

Gnomad4 EAS exome AF: 0.142

Gnomad4 SAS exome AF: 0.174

Gnomad4 FIN exome AF: 0.138

Gnomad4 NFE exome AF: 0.153

Gnomad4 OTH exome AF: 0.161

GnomAD4 genome AF: 0.0740 AC: 9715 AN: 131314 Hom.: 806 Cov.: 29 AF XY: 0.0726 AC XY: 4589 AN XY: 63170

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0407

Gnomad4 ASJ AF: 0.0185

Gnomad4 EAS AF: 0.00433

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.00909

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.0625

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

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs36056285; hg19: chr3-52621586;