rs10521289

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005611.4(RBL2):​c.573-746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 151,578 control chromosomes in the GnomAD database, including 627 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 0.052 ( 627 hom., cov: 33)

Consequence

RBL2
NM_005611.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.214
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RBL2NM_005611.4 linkc.573-746G>A intron_variant Intron 3 of 21 ENST00000262133.11 NP_005602.3 Q08999-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RBL2ENST00000262133.11 linkc.573-746G>A intron_variant Intron 3 of 21 1 NM_005611.4 ENSP00000262133.6 Q08999-1

Frequencies

GnomAD3 genomes
AF:
0.0521
AC:
7894
AN:
151458
Hom.:
618
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.177
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0255
Gnomad ASJ
AF:
0.0121
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.000416
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0446
Gnomad NFE
AF:
0.00202
Gnomad OTH
AF:
0.0383
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0524
AC:
7937
AN:
151578
Hom.:
627
Cov.:
33
AF XY:
0.0506
AC XY:
3753
AN XY:
74108
show subpopulations
Gnomad4 AFR
AF:
0.177
Gnomad4 AMR
AF:
0.0255
Gnomad4 ASJ
AF:
0.0121
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.000417
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00202
Gnomad4 OTH
AF:
0.0379
Alfa
AF:
0.0192
Hom.:
83
Bravo
AF:
0.0589
Asia WGS
AF:
0.0140
AC:
50
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.9
DANN
Benign
0.27

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10521289; hg19: chr16-53480208; API