16-24553558-G-GTA

Position:

• chr16-24553558-G-GTA

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6 BS2

The NM_006910.5(RBBP6):​c.348+17_348+18dupAT variant causes a intron change. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00057 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0017 (0 hom.)
• Consequence: RBBP6 NM_006910.5 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 4.87

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP6: Variant 16-24553558-G-GTA is Benign according to our data. Variant chr16-24553558-G-GTA is described in ClinVar as [Likely_benign]. Clinvar id is 2443233.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 85 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBBP6	NM_006910.5	c.348+17_348+18dupAT		intron_variant		ENST00000319715.10	NP_008841.2
RBBP6	NM_018703.4	c.348+17_348+18dupAT		intron_variant			NP_061173.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBBP6	ENST00000319715.10	c.348+17_348+18dupAT		intron_variant		1	NM_006910.5	ENSP00000317872.4

Frequencies

GnomAD3 genomes AF: 0.000568 AC: 85 AN: 149770 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000534

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000779

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.0000984

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000894

Gnomad OTH AF: 0.00146

GnomAD4 exome AF: 0.00166 AC: 2136 AN: 1283108 Hom.: 0 Cov.: 0 AF XY: 0.00163 AC XY: 1046 AN XY: 640428

Gnomad4 AFR exome AF: 0.000372

Gnomad4 AMR exome AF: 0.000931

Gnomad4 ASJ exome AF: 0.000785

Gnomad4 EAS exome AF: 0.000940

Gnomad4 SAS exome AF: 0.000693

Gnomad4 FIN exome AF: 0.000545

Gnomad4 NFE exome AF: 0.00193

Gnomad4 OTH exome AF: 0.00113

GnomAD4 genome AF: 0.000567 AC: 85 AN: 149890 Hom.: 0 Cov.: 0 AF XY: 0.000492 AC XY: 36 AN XY: 73164

Gnomad4 AFR AF: 0.000195

Gnomad4 AMR AF: 0.000533

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000781

Gnomad4 SAS AF: 0.000210

Gnomad4 FIN AF: 0.0000984

Gnomad4 NFE AF: 0.000894

Gnomad4 OTH AF: 0.00145

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

not specified Benign:1

Likely benign, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

Dec 16, 2022

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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: rs72133882; hg19: chr16-24564879;