chr3-52550699-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000707071.1(PBRM1):c.4725+48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,582,072 control chromosomes in the GnomAD database, including 135,593 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.42 ( 13402 hom., cov: 32)
Exomes 𝑓: 0.41 ( 122191 hom. )
Consequence
PBRM1
ENST00000707071.1 intron
ENST00000707071.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.279
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 3-52550699-A-G is Benign according to our data. Variant chr3-52550699-A-G is described in ClinVar as [Benign]. Clinvar id is 1178095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBRM1 | NM_001405607.1 | c.4725+48T>C | intron_variant | ENST00000707071.1 | |||
PBRM1 | NR_175959.1 | n.4869+48T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBRM1 | ENST00000707071.1 | c.4725+48T>C | intron_variant | NM_001405607.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.416 AC: 63198AN: 151970Hom.: 13388 Cov.: 32
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GnomAD3 exomes AF: 0.419 AC: 102049AN: 243404Hom.: 22082 AF XY: 0.408 AC XY: 53816AN XY: 131760
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GnomAD4 exome AF: 0.410 AC: 586301AN: 1429984Hom.: 122191 Cov.: 23 AF XY: 0.405 AC XY: 288921AN XY: 712700
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GnomAD4 genome AF: 0.416 AC: 63264AN: 152088Hom.: 13402 Cov.: 32 AF XY: 0.416 AC XY: 30953AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at