3-52587806-T-TTTC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.498

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]

ACMG classification

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
PBRM1	NM_001405607.1	c.3011-297_3011-296insGAA		intron_variant		ENST00000707071.1
PBRM1	NR_175959.1	n.3188-297_3188-296insGAA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PBRM1	ENST00000707071.1	c.3011-297_3011-296insGAA		intron_variant			NM_001405607.1	A1

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146003 AN: 151822 Hom.: 70245 Cov.: 0

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

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4044904; hg19: chr3-52621822;