3-52587570-C-CT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
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
ENST00000707071.1 intron
Scores
Not classified
Clinical Significance
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]
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ACMG classification
Classification made for transcript
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: 9708AN: 131332Hom.: 806 Cov.: 29
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GnomAD4 exome AF: 0.155 AC: 90529AN: 584702Hom.: 1 AF XY: 0.156 AC XY: 46906AN XY: 301190
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GnomAD4 genome AF: 0.0740 AC: 9715AN: 131314Hom.: 806 Cov.: 29 AF XY: 0.0726 AC XY: 4589AN XY: 63170
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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 submitter | clinical testing | GeneDx | Aug 15, 2019 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at