chr3-25461005-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000965.5(RARB):​c.158-188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,230 control chromosomes in the GnomAD database, including 273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.041 ( 273 hom., cov: 32)

Consequence

RARB
NM_000965.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.385
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 3-25461005-C-T is Benign according to our data. Variant chr3-25461005-C-T is described in ClinVar as [Benign]. Clinvar id is 1294921.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RARBNM_000965.5 linkuse as main transcriptc.158-188C>T intron_variant ENST00000330688.9 NP_000956.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RARBENST00000330688.9 linkuse as main transcriptc.158-188C>T intron_variant 1 NM_000965.5 ENSP00000332296 P1P10826-2

Frequencies

GnomAD3 genomes
AF:
0.0405
AC:
6165
AN:
152112
Hom.:
272
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0303
Gnomad ASJ
AF:
0.0109
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00704
Gnomad FIN
AF:
0.00406
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0127
Gnomad OTH
AF:
0.0363
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0406
AC:
6182
AN:
152230
Hom.:
273
Cov.:
32
AF XY:
0.0395
AC XY:
2942
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.0303
Gnomad4 ASJ
AF:
0.0109
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00704
Gnomad4 FIN
AF:
0.00406
Gnomad4 NFE
AF:
0.0127
Gnomad4 OTH
AF:
0.0360
Alfa
AF:
0.0298
Hom.:
19
Bravo
AF:
0.0463
Asia WGS
AF:
0.0120
AC:
42
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 14, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.5
DANN
Benign
0.65

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: rs74820342; hg19: chr3-25502496; API