rs11271404

Variant summary

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

The NM_000965.5(RARB):​c.306+6163_306+6201delACAATCATAGCAAGCCAACGCCACTTATCCAGTGAACCA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 16476 hom., cov: 0)

Consequence

RARB
NM_000965.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

0 publications found
Variant links:
Genes affected
RARB (HGNC:9865): (retinoic acid receptor beta) This gene encodes retinoic acid receptor beta, a member of the thyroid-steroid hormone receptor superfamily of nuclear transcriptional regulators. This receptor localizes to the cytoplasm and to subnuclear compartments. It binds retinoic acid, the biologically active form of vitamin A which mediates cellular signalling in embryonic morphogenesis, cell growth and differentiation. It is thought that this protein limits growth of many cell types by regulating gene expression. The gene was first identified in a hepatocellular carcinoma where it flanks a hepatitis B virus integration site. Alternate promoter usage and differential splicing result in multiple transcript variants. [provided by RefSeq, Mar 2014]
RARB Gene-Disease associations (from GenCC):
  • microphthalmia, syndromic 12
    Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, Baylor College of Medicine Research Center
  • Matthew-Wood syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RARBNM_000965.5 linkc.306+6163_306+6201delACAATCATAGCAAGCCAACGCCACTTATCCAGTGAACCA intron_variant Intron 2 of 7 ENST00000330688.9 NP_000956.2 P10826-2F1D8S6Q86UC5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RARBENST00000330688.9 linkc.306+6163_306+6201delACAATCATAGCAAGCCAACGCCACTTATCCAGTGAACCA intron_variant Intron 2 of 7 1 NM_000965.5 ENSP00000332296.4 P10826-2

Frequencies

GnomAD3 genomes
AF:
0.465
AC:
70210
AN:
151138
Hom.:
16460
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.443
Gnomad AMI
AF:
0.512
Gnomad AMR
AF:
0.482
Gnomad ASJ
AF:
0.387
Gnomad EAS
AF:
0.669
Gnomad SAS
AF:
0.528
Gnomad FIN
AF:
0.435
Gnomad MID
AF:
0.442
Gnomad NFE
AF:
0.463
Gnomad OTH
AF:
0.445
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.465
AC:
70269
AN:
151250
Hom.:
16476
Cov.:
0
AF XY:
0.467
AC XY:
34478
AN XY:
73862
show subpopulations
African (AFR)
AF:
0.443
AC:
18276
AN:
41248
American (AMR)
AF:
0.482
AC:
7332
AN:
15212
Ashkenazi Jewish (ASJ)
AF:
0.387
AC:
1341
AN:
3462
East Asian (EAS)
AF:
0.670
AC:
3380
AN:
5046
South Asian (SAS)
AF:
0.527
AC:
2523
AN:
4792
European-Finnish (FIN)
AF:
0.435
AC:
4554
AN:
10474
Middle Eastern (MID)
AF:
0.451
AC:
129
AN:
286
European-Non Finnish (NFE)
AF:
0.463
AC:
31333
AN:
67736
Other (OTH)
AF:
0.449
AC:
939
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.427
Heterozygous variant carriers
0
1961
3922
5883
7844
9805
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
650
1300
1950
2600
3250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.468
Hom.:
1784
Asia WGS
AF:
0.581
AC:
2019
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.0
Mutation Taster
=27/73
disease causing (long InDel)

Splicing

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

Publications

Other links and lift over

dbSNP: rs11271404; hg19: chr3-25508994; API