chr3-52587806-T-TTTC

Variant summary

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

The ENST00000707071.1(PBRM1):​c.3011-297_3011-296insGAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.96 ( 70302 hom., cov: 0)

Consequence

PBRM1
ENST00000707071.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.498
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 3-52587806-T-TTTC is Benign according to our data. Variant chr3-52587806-T-TTTC is described in ClinVar as [Benign]. Clinvar id is 1220693.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PBRM1NM_001405607.1 linkuse as main transcriptc.3011-297_3011-296insGAA intron_variant ENST00000707071.1
PBRM1NR_175959.1 linkuse as main transcriptn.3188-297_3188-296insGAA intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PBRM1ENST00000707071.1 linkuse as main transcriptc.3011-297_3011-296insGAA intron_variant NM_001405607.1 A1

Frequencies

GnomAD3 genomes
AF:
0.962
AC:
146003
AN:
151822
Hom.:
70245
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.989
Gnomad AMI
AF:
0.984
Gnomad AMR
AF:
0.977
Gnomad ASJ
AF:
0.971
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.957
Gnomad FIN
AF:
0.968
Gnomad MID
AF:
0.984
Gnomad NFE
AF:
0.937
Gnomad OTH
AF:
0.965
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.962
AC:
146120
AN:
151940
Hom.:
70302
Cov.:
0
AF XY:
0.963
AC XY:
71523
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.989
Gnomad4 AMR
AF:
0.977
Gnomad4 ASJ
AF:
0.971
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.957
Gnomad4 FIN
AF:
0.968
Gnomad4 NFE
AF:
0.937
Gnomad4 OTH
AF:
0.965
Alfa
AF:
0.920
Hom.:
2865
Bravo
AF:
0.965
Asia WGS
AF:
0.988
AC:
3431
AN:
3474

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 19, 2021- -

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: rs4044904; hg19: chr3-52621822; API