rs72133882

Variant names:

• chr16-24553558-GTATATA-G
• rs72133882
• NM_006910.5:c.348+13_348+18delATATAT

Your query was ambiguous. Multiple possible variants found:

• chr16-24553558-GTATATA-G
• chr16-24553558-GTATATA-GTA
• chr16-24553558-GTATATA-GTATA
• chr16-24553558-GTATATA-GTATATATA
• chr16-24553558-GTATATA-GTATATATATA
• chr16-24553558-GTATATA-GTATATATATATA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006910.5(RBBP6):​c.348+13_348+18delATATAT variant causes a intron change. The variant allele was found at a frequency of 0.0000178 in 1,291,732 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000018 (0 hom.)
• Consequence: RBBP6 NM_006910.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.83
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBBP6	NM_006910.5	c.348+13_348+18delATATAT		intron_variant	Intron 4 of 17	ENST00000319715.10	NP_008841.2
RBBP6	NM_018703.4	c.348+13_348+18delATATAT		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	c.348+13_348+18delATATAT		intron_variant	Intron 4 of 17	1	NM_006910.5	ENSP00000317872.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.0000232 AC: 4 AN: 172582 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000428

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000246

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000178 AC: 23 AN: 1291732 Hom.: 0 AF XY: 0.0000124 AC XY: 8 AN XY: 644488

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000745 AC: 2 AN: 26854

American (AMR) AF: 0.0000266 AC: 1 AN: 37656

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23028

East Asian (EAS) AF: 0.00 AC: 0 AN: 37458

South Asian (SAS) AF: 0.0000424 AC: 3 AN: 70806

European-Finnish (FIN) AF: 0.0000418 AC: 2 AN: 47894

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4030

European-Non Finnish (NFE) AF: 0.0000141 AC: 14 AN: 990832

Other (OTH) AF: 0.0000188 AC: 1 AN: 53174

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.8
Mutation Taster		=92/8	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs72133882; hg19: chr16-24564879;