3-52562157-TA-T

Variant summary

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

The ENST00000707071.1(PBRM1):c.4132-190del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.42 (13069 hom., cov: 0)
• Consequence: PBRM1 ENST00000707071.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.108

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]

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-52562157-TA-T is Benign according to our data. Variant chr3-52562157-TA-T is described in ClinVar as [Benign]. Clinvar id is 1246864.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PBRM1	NM_001405607.1	c.4132-190del		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1	n.4309-190del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1	c.4132-190del		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 62180 AN: 147970 Hom.: 13057 Cov.: 0

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.420 AC: 62242 AN: 148076 Hom.: 13069 Cov.: 0 AF XY: 0.421 AC XY: 30367 AN XY: 72082

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.435

Bravo AF: 0.425

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: rs11295229; hg19: chr3-52596173;