Genetic Variant RBBP6:c.348+17_348+18delAT (chr16-24553558-GTA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006910.5(RBBP6):c.348+17_348+18delAT variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 29528 hom., cov: 0)

Exomes 𝑓: 0.51 ( 108973 hom. )

Failed GnomAD Quality Control

Consequence

RBBP6
NM_006910.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.83

Publications

7 publications found

Variant links:

Genes affected

RBBP6 (HGNC:9889): (RB binding protein 6, ubiquitin ligase) The retinoblastoma tumor suppressor (pRB) protein binds with many other proteins. In various human cancers, pRB suppresses cellular proliferation and is inactivated. Cell cycle-dependent phosphorylation regulates the activity of pRB. This gene encodes a protein which binds to underphosphorylated but not phosphorylated pRB. Multiple alternatively spliced transcript variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

RBBP6 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBBP6	NM_006910.5 link	c.348+17_348+18delAT		intron_variant	Intron 4 of 17	ENST00000319715.10	NP_008841.2
RBBP6	NM_018703.4 link	c.348+17_348+18delAT		intron_variant	Intron 4 of 16		NP_061173.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBBP6	ENST00000319715.10 link	c.348+17_348+18delAT		intron_variant	Intron 4 of 17	1	NM_006910.5	ENSP00000317872.4		Q7Z6E9-1

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

91848

AN:

149612

Hom.:

29484

Cov.:

show subpopulations

Gnomad AFR

AF:

0.817

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.708

Gnomad FIN

AF:

0.531

Gnomad MID

AF:

0.650

Gnomad NFE

AF:

0.516

Gnomad OTH

AF:

0.612

GnomAD2 exomes

AF:

0.546

AC:

94170

AN:

172582

AF XY:

0.547

show subpopulations

Gnomad AFR exome

AF:

0.711

Gnomad AMR exome

AF:

0.541

Gnomad ASJ exome

AF:

0.557

Gnomad EAS exome

AF:

0.442

Gnomad FIN exome

AF:

0.553

Gnomad NFE exome

AF:

0.527

Gnomad OTH exome

AF:

0.538

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.506

AC:

622770

AN:

1231146

Hom.:

108973

AF XY:

0.509

AC XY:

312231

AN XY:

613698

show subpopulations

African (AFR)

AF:

0.699

AC:

18678

AN:

26714

American (AMR)

AF:

0.524

AC:

19138

AN:

36538

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

11814

AN:

21790

East Asian (EAS)

AF:

0.445

AC:

14655

AN:

32896

South Asian (SAS)

AF:

0.599

AC:

41708

AN:

69572

European-Finnish (FIN)

AF:

0.517

AC:

23283

AN:

44994

Middle Eastern (MID)

AF:

0.550

AC:

2139

AN:

3886

European-Non Finnish (NFE)

AF:

0.492

AC:

464698

AN:

944096

Other (OTH)

AF:

0.526

AC:

26657

AN:

50660

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.561

Heterozygous variant carriers

14539

29078

43618

58157

72696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.614

AC:

91941

AN:

149732

Hom.:

29528

Cov.:

AF XY:

0.616

AC XY:

45006

AN XY:

73062

show subpopulations

African (AFR)

AF:

0.817

AC:

33502

AN:

41004

American (AMR)

AF:

0.615

AC:

9207

AN:

14982

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

2044

AN:

3436

East Asian (EAS)

AF:

0.396

AC:

2024

AN:

5114

South Asian (SAS)

AF:

0.709

AC:

3376

AN:

4762

European-Finnish (FIN)

AF:

0.531

AC:

5381

AN:

10142

Middle Eastern (MID)

AF:

0.664

AC:

194

AN:

292

European-Non Finnish (NFE)

AF:

0.516

AC:

34572

AN:

67024

Other (OTH)

AF:

0.614

AC:

1273

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1659

3318

4976

6635

8294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.454

Hom.:

1776

Bravo

AF:

0.626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

5.8

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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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16-24553558-GTATATA-GTATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over