rs9921587

Positions:

• chr16-53441738-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000262133.11(RBL2):​c.372-920A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,054 control chromosomes in the GnomAD database, including 25,038 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (25038 hom., cov: 31)
• Consequence: RBL2 ENST00000262133.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

Genes affected

RBL2 (HGNC:9894): (RB transcriptional corepressor like 2) Enables promoter-specific chromatin binding activity. Involved in regulation of lipid kinase activity. Acts upstream of or within negative regulation of gene expression. Located in chromosome; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBL2	NM_005611.4	c.372-920A>G		intron_variant		ENST00000262133.11	NP_005602.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBL2	ENST00000262133.11	c.372-920A>G		intron_variant		1	NM_005611.4	ENSP00000262133	P1
RBL2	ENST00000544405.6	c.150-920A>G		intron_variant		2		ENSP00000443744
RBL2	ENST00000567964.6	c.-22-920A>G		intron_variant		5		ENSP00000462464
RBL2	ENST00000680543.1	n.511-920A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82739 AN: 151936 Hom.: 24985 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.545 AC: 82847 AN: 152054 Hom.: 25038 Cov.: 31 AF XY: 0.534 AC XY: 39716 AN XY: 74328

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.553

Alfa AF: 0.490 Hom.: 8912

Bravo AF: 0.558

Asia WGS AF: 0.426 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.80

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

LitVar

Other links and lift over

dbSNP: rs9921587; hg19: chr16-53475650; COSMIC: COSV50878746; COSMIC: COSV50878746;