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GeneBe

rs17016462

Variant summary

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

The NM_000965.5(RARB):c.306+13284A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 152,310 control chromosomes in the GnomAD database, including 247 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 0.031 ( 247 hom., cov: 33)

Consequence

RARB
NM_000965.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.669
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]

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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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RARBNM_000965.5 linkuse as main transcriptc.306+13284A>T intron_variant ENST00000330688.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RARBENST00000330688.9 linkuse as main transcriptc.306+13284A>T intron_variant 1 NM_000965.5 P1P10826-2

Frequencies

GnomAD3 genomes
AF:
0.0309
AC:
4701
AN:
152192
Hom.:
246
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0183
Gnomad AMI
AF:
0.0208
Gnomad AMR
AF:
0.0329
Gnomad ASJ
AF:
0.0493
Gnomad EAS
AF:
0.256
Gnomad SAS
AF:
0.0431
Gnomad FIN
AF:
0.0591
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0152
Gnomad OTH
AF:
0.0258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0308
AC:
4691
AN:
152310
Hom.:
247
Cov.:
33
AF XY:
0.0346
AC XY:
2580
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0183
Gnomad4 AMR
AF:
0.0327
Gnomad4 ASJ
AF:
0.0493
Gnomad4 EAS
AF:
0.255
Gnomad4 SAS
AF:
0.0417
Gnomad4 FIN
AF:
0.0591
Gnomad4 NFE
AF:
0.0152
Gnomad4 OTH
AF:
0.0269
Alfa
AF:
0.0190
Hom.:
3
Bravo
AF:
0.0306
Asia WGS
AF:
0.136
AC:
471
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
9.7
Dann
Benign
0.76

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: rs17016462; hg19: chr3-25516116; API