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GeneBe

3-52550218-AAAAAC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.18
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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
PBRM1NM_001405607.1 linkuse as main transcriptc.4942+198_4942+202del intron_variant ENST00000707071.1
PBRM1NR_175959.1 linkuse as main transcriptn.5086+198_5086+202del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PBRM1ENST00000707071.1 linkuse as main transcriptc.4942+198_4942+202del intron_variant NM_001405607.1 A1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.116
AC:
17687
AN:
151938
Hom.:
2566
Cov.:
31
show subpopulations
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.117
AC:
17735
AN:
152056
Hom.:
2577
Cov.:
31
AF XY:
0.113
AC XY:
8431
AN XY:
74364
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 23, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs144534586; hg19: chr3-52584234; API