dbSNP rs13083798: PBRM1:c.1864-276T>C (chr3-52615732-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001405607.1(PBRM1):c.1864-276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,874 control chromosomes in the GnomAD database, including 20,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 20087 hom., cov: 31)

Consequence

PBRM1
NM_001405607.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.142

Publications

44 publications found

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]

PBRM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 3-52615732-A-G is Benign according to our data. Variant chr3-52615732-A-G is described in ClinVar as Benign. ClinVar VariationId is 1232523.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001405607.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PBRM1	NM_001405607.1	MANE Select	c.1864-276T>C	intron	N/A	NP_001392536.1	A0A9L9PXL4
PBRM1	NM_001405601.1		c.1864-276T>C	intron	N/A	NP_001392530.1	A0A9L9PXL4
PBRM1	NM_001405598.1		c.1846-276T>C	intron	N/A	NP_001392527.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PBRM1	ENST00000707071.1	MANE Select	c.1864-276T>C	intron	N/A	ENSP00000516722.1	A0A9L9PXL4
PBRM1	ENST00000296302.11	TSL:1	c.1819-276T>C	intron	N/A	ENSP00000296302.7	Q86U86-1
PBRM1	ENST00000409114.7	TSL:1	c.1864-276T>C	intron	N/A	ENSP00000386643.3	Q86U86-8

Frequencies

GnomAD3 genomes

AF:

0.510

AC:

77438

AN:

151754

Hom.:

20067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.539

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.593

Gnomad ASJ

AF:

0.519

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.499

Gnomad OTH

AF:

0.518

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.510

AC:

77511

AN:

151874

Hom.:

20087

Cov.:

AF XY:

0.507

AC XY:

37604

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.539

AC:

22332

AN:

41404

American (AMR)

AF:

0.593

AC:

9055

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.519

AC:

1799

AN:

3468

East Asian (EAS)

AF:

0.456

AC:

2347

AN:

5148

South Asian (SAS)

AF:

0.301

AC:

1448

AN:

4818

European-Finnish (FIN)

AF:

0.462

AC:

4865

AN:

10538

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.499

AC:

33897

AN:

67920

Other (OTH)

AF:

0.523

AC:

1102

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1922

3843

5765

7686

9608

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.509

Hom.:

27837

Bravo

AF:

0.525

Asia WGS

AF:

0.431

AC:

1499

AN:

3476

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.2

(source)

DANN

Benign

0.65

PhyloP100

0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over