3-52548429-A-AT

Variant summary

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

The ENST00000707071.1(PBRM1):c.4943-195_4943-194insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 145,466 control chromosomes in the GnomAD database, including 204 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.033 (204 hom., cov: 32)
• Consequence: PBRM1 ENST00000707071.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.246

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 3-52548429-A-AT is Benign according to our data. Variant chr3-52548429-A-AT is described in ClinVar as [Benign]. Clinvar id is 1233642.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PBRM1	NM_001405607.1	c.4943-195_4943-194insA		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1	n.5087-195_5087-194insA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1	c.4943-195_4943-194insA		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 4788 AN: 145426 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.00594

Gnomad EAS AF: 0.00139

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.00987

Gnomad NFE AF: 0.00607

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0330 AC: 4801 AN: 145466 Hom.: 204 Cov.: 32 AF XY: 0.0324 AC XY: 2292 AN XY: 70796

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.0110

Gnomad4 ASJ AF: 0.00594

Gnomad4 EAS AF: 0.00139

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.00607

Gnomad4 OTH AF: 0.0285

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: rs372814552; hg19: chr3-52582445;