1-165414524-C-T

Variant summary

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

The NM_006917.5(RXRG):​c.622+2517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,224 control chromosomes in the GnomAD database, including 1,733 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 0.15 ( 1733 hom., cov: 33)

Consequence

RXRG
NM_006917.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260
Variant links:
Genes affected
RXRG (HGNC:10479): (retinoid X receptor gamma) This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the antiproliferative effects of retinoic acid (RA). This receptor forms dimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene is expressed at significantly lower levels in non-small cell lung cancer cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2010]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RXRGNM_006917.5 linkc.622+2517G>A intron_variant Intron 4 of 9 ENST00000359842.10 NP_008848.1 P48443F1D8Q7
RXRGNM_001256570.2 linkc.253+2517G>A intron_variant Intron 5 of 10 NP_001243499.1 A0A087WZ88F1T097
RXRGNM_001256571.2 linkc.253+2517G>A intron_variant Intron 3 of 8 NP_001243500.1 P48443A0A087WZ88

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RXRGENST00000359842.10 linkc.622+2517G>A intron_variant Intron 4 of 9 1 NM_006917.5 ENSP00000352900.5 P48443
RXRGENST00000619224.1 linkc.253+2517G>A intron_variant Intron 5 of 10 1 ENSP00000482458.1 A0A087WZ88
RXRGENST00000470566.1 linkn.547+2517G>A intron_variant Intron 3 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.148
AC:
22570
AN:
152104
Hom.:
1731
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.126
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.118
Gnomad EAS
AF:
0.216
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.154
Gnomad OTH
AF:
0.137
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.148
AC:
22586
AN:
152224
Hom.:
1733
Cov.:
33
AF XY:
0.152
AC XY:
11281
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.126
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.118
Gnomad4 EAS
AF:
0.216
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.177
Gnomad4 NFE
AF:
0.154
Gnomad4 OTH
AF:
0.138
Alfa
AF:
0.154
Hom.:
879
Bravo
AF:
0.142
Asia WGS
AF:
0.211
AC:
733
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.2
DANN
Benign
0.68

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: rs157864; hg19: chr1-165383761; API