3-52550218-AAAAAC-A

Position:

• chr3-52550218-AAAAAC-A

Variant summary

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

The ENST00000707071.1(PBRM1):​c.4942+198_4942+202del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,056 control chromosomes in the GnomAD database, including 2,577 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (2577 hom., cov: 31)
• Consequence: PBRM1 ENST00000707071.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.18

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 3-52550218-AAAAAC-A is Benign according to our data. Variant chr3-52550218-AAAAAC-A is described in ClinVar as [Benign]. Clinvar id is 1283771.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PBRM1	NM_001405607.1	c.4942+198_4942+202del		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1	n.5086+198_5086+202del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1	c.4942+198_4942+202del		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17687 AN: 151938 Hom.: 2566 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.00763

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.117 AC: 17735 AN: 152056 Hom.: 2577 Cov.: 31 AF XY: 0.113 AC XY: 8431 AN XY: 74364

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0620

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.00250

Gnomad4 SAS AF: 0.0611

Gnomad4 FIN AF: 0.00763

Gnomad4 NFE AF: 0.0268

Gnomad4 OTH AF: 0.0946

Bravo AF: 0.132

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 23, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs144534586; hg19: chr3-52584234;