3-52587570-C-CT

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.167
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]

Genome browser will be placed here

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
PBRM1NM_001405607.1 linkuse as main transcriptc.3011-61_3011-60insA intron_variant ENST00000707071.1
PBRM1NR_175959.1 linkuse as main transcriptn.3188-61_3188-60insA intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PBRM1ENST00000707071.1 linkuse as main transcriptc.3011-61_3011-60insA intron_variant NM_001405607.1 A1

Frequencies

GnomAD3 genomes
AF:
0.0739
AC:
9708
AN:
131332
Hom.:
806
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.00352
Gnomad AMR
AF:
0.0408
Gnomad ASJ
AF:
0.0185
Gnomad EAS
AF:
0.00432
Gnomad SAS
AF:
0.0392
Gnomad FIN
AF:
0.00909
Gnomad MID
AF:
0.0468
Gnomad NFE
AF:
0.0247
Gnomad OTH
AF:
0.0623
GnomAD4 exome
AF:
0.155
AC:
90529
AN:
584702
Hom.:
1
AF XY:
0.156
AC XY:
46906
AN XY:
301190
show subpopulations
Gnomad4 AFR exome
AF:
0.234
Gnomad4 AMR exome
AF:
0.150
Gnomad4 ASJ exome
AF:
0.152
Gnomad4 EAS exome
AF:
0.142
Gnomad4 SAS exome
AF:
0.174
Gnomad4 FIN exome
AF:
0.138
Gnomad4 NFE exome
AF:
0.153
Gnomad4 OTH exome
AF:
0.161
GnomAD4 genome
AF:
0.0740
AC:
9715
AN:
131314
Hom.:
806
Cov.:
29
AF XY:
0.0726
AC XY:
4589
AN XY:
63170
show subpopulations
Gnomad4 AFR
AF:
0.205
Gnomad4 AMR
AF:
0.0407
Gnomad4 ASJ
AF:
0.0185
Gnomad4 EAS
AF:
0.00433
Gnomad4 SAS
AF:
0.0392
Gnomad4 FIN
AF:
0.00909
Gnomad4 NFE
AF:
0.0247
Gnomad4 OTH
AF:
0.0625

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 testingGeneDxAug 15, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs36056285; hg19: chr3-52621586; API