rs142726131
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The ENST00000707071.1(PBRM1):c.4901C>T(p.Ala1634Val) variant causes a missense change. The variant allele was found at a frequency of 0.000121 in 1,556,196 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
PBRM1
ENST00000707071.1 missense
ENST00000707071.1 missense
Scores
2
4
11
Clinical Significance
Conservation
PhyloP100: 6.74
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 -7 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, PBRM1
BP4
?
Computational evidence support a benign effect (MetaRNN=0.037751257).
BS2
?
High AC in GnomAd4 at 16 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBRM1 | NM_001405607.1 | c.4901C>T | p.Ala1634Val | missense_variant | 31/32 | ENST00000707071.1 | |
PBRM1 | NR_175959.1 | n.5045C>T | non_coding_transcript_exon_variant | 31/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBRM1 | ENST00000707071.1 | c.4901C>T | p.Ala1634Val | missense_variant | 31/32 | NM_001405607.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152154Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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152154
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32
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GnomAD3 exomes AF: 0.000194 AC: 41AN: 210886Hom.: 0 AF XY: 0.000273 AC XY: 31AN XY: 113482
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GnomAD4 exome AF: 0.000123 AC: 173AN: 1403924Hom.: 0 Cov.: 32 AF XY: 0.000140 AC XY: 97AN XY: 693870
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152272Hom.: 1 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74462
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ExAC
?
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30
Asia WGS
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2
AN:
3478
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
D;D;D;D;D;D;D;D
Vest4
MVP
MPC
1.3
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at