rs104894891
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_000475.5(NR0B1):c.513G>T(p.Trp171Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000944 in 1,059,688 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 9.4e-7 ( 0 hom. 0 hem. )
Consequence
NR0B1
NM_000475.5 missense
NM_000475.5 missense
Scores
3
8
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.348
Publications
1 publications found
Genes affected
NR0B1 (HGNC:7960): (nuclear receptor subfamily 0 group B member 1) This gene encodes a protein that contains a DNA-binding domain. The encoded protein acts as a dominant-negative regulator of transcription which is mediated by the retinoic acid receptor. This protein also functions as an anti-testis gene by acting antagonistically to Sry. Mutations in this gene result in both X-linked congenital adrenal hypoplasia and hypogonadotropic hypogonadism. [provided by RefSeq, Jul 2008]
NR0B1 Gene-Disease associations (from GenCC):
- X-linked adrenal hypoplasia congenitaInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Myriad Women’s Health, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- 46,XY sex reversal 2Inheritance: XL Classification: MODERATE Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
24
GnomAD2 exomes AF: 0.00000600 AC: 1AN: 166612 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
166612
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 9.44e-7 AC: 1AN: 1059688Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 354280 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1059688
Hom.:
Cov.:
34
AF XY:
AC XY:
0
AN XY:
354280
show subpopulations
African (AFR)
AF:
AC:
0
AN:
24461
American (AMR)
AF:
AC:
0
AN:
30237
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18173
East Asian (EAS)
AF:
AC:
0
AN:
26434
South Asian (SAS)
AF:
AC:
0
AN:
50452
European-Finnish (FIN)
AF:
AC:
1
AN:
38898
Middle Eastern (MID)
AF:
AC:
0
AN:
3980
European-Non Finnish (NFE)
AF:
AC:
0
AN:
823197
Other (OTH)
AF:
AC:
0
AN:
43856
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
24
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Pathogenic
D
MutationAssessor
Benign
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of catalytic residue at W172 (P = 0.0042);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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