chr1:161202605:G>A Detail (hg19) (NR1I3)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr1:161,202,605-161,202,605
hg38	chr1:161,232,815-161,232,815 View the variant detail on this assembly version.

HGVS

NR1I3

Type	Transcript	Protein
RefSeq	NM_001077470.2:c.453C>T	NP_001070938.1:p.Pro151=
	NM_001077471.2:c.540C>T	NP_001070939.1:p.Pro180=
	NM_001077476.2:c.453C>T	NP_001070944.1:p.Pro151=
	NM_001077472.2:c.453C>T	NP_001070940.1:p.Pro151=
	NM_001077477.2:c.453C>T	NP_001070945.1:p.Pro151=
	NM_001077469.2:c.540C>T	NP_001070937.1:p.Pro180=
	NM_001077478.2:c.540C>T	NP_001070946.1:p.Pro180=
	NM_001077480.2:c.540C>T	NP_001070948.1:p.Pro180=
	NM_001077481.2:c.540C>T	NP_001070949.1:p.Pro180=
	NM_001077482.2:c.540C>T	NP_001070950.1:p.Pro180=
	NM_005122.4:c.540C>T	NP_005113.1:p.Pro180=
	NM_001077473.2:c.453C>T	NP_001070941.1:p.Pro151=
	NM_001077479.2:c.453C>T	NP_001070947.1:p.Pro151=
	NM_001077474.2:c.540C>T	NP_001070942.1:p.Pro180=
	NM_001077475.2:c.453C>T	NP_001070943.1:p.Pro151=
Ensemble	ENST00000515452.1:c.540C>T	ENST00000515452.1:p.Pro180=
	ENST00000367983.9:c.540C>T	ENST00000367983.9:p.Pro180=
	ENST00000506209.5:c.453C>T	ENST00000506209.5:p.Pro151=
	ENST00000504010.5:c.453C>T	ENST00000504010.5:p.Pro151=
	ENST00000508387.5:c.152-1341C>T
	ENST00000367984.8:c.540C>T	ENST00000367984.8:p.Pro180=
	ENST00000511748.5:c.152-1341C>T
	ENST00000442691.6:c.540C>T	ENST00000442691.6:p.Pro180=
	ENST00000508740.5:c.453C>T	ENST00000508740.5:p.Pro151=
	ENST00000367982.8:c.540C>T	ENST00000367982.8:p.Pro180=
	ENST00000367981.7:c.453C>T	ENST00000367981.7:p.Pro151=
	ENST00000428574.6:c.540C>T	ENST00000428574.6:p.Pro180=
	ENST00000437437.6:c.453C>T	ENST00000437437.6:p.Pro151=
	ENST00000628566.2:c.*10C>T
	ENST00000367985.7:c.540C>T	ENST00000367985.7:p.Pro180=
	ENST00000502985.5:c.239-1341C>T
	ENST00000367980.6:c.540C>T	ENST00000367980.6:p.Pro180=
	ENST00000412844.6:c.453C>T	ENST00000412844.6:p.Pro151=
	ENST00000511676.5:c.453C>T	ENST00000511676.5:p.Pro151=
	ENST00000505005.5:c.540C>T	ENST00000505005.5:p.Pro180=
	ENST00000512372.5:c.453C>T	ENST00000512372.5:p.Pro151=
	ENST00000511944.5:c.239-1341C>T
	ENST00000367979.6:c.540C>T	ENST00000367979.6:p.Pro180=
	ENST00000515621.5:c.315C>T	ENST00000515621.5:p.Pro105=

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.536
	ToMMo:0.535
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.536

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

NR1I3

Type	Database	ID	Link
Gene	MIM	603881	OMIM
	HGNC	7969	HGNC
	Ensembl	ENSG00000143257	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv3520365	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2014-10-02	criteria provided, single submitter	not specified	germline	Detail
Benign	2019-10-18	criteria provided, single submitter	NR1I3-related disorder	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	HIV Infections	In this study, we investigated the effects of CYP2B6 516G>T (rs3745274), CYP2...	BeFree	24831655	Detail

Annotation

Annotations

Descrption	Source	Links
NM_005122.5(NR1I3):c.540C>T (p.Pro180=) AND not specified	ClinVar	Detail
NM_005122.5(NR1I3):c.540C>T (p.Pro180=) AND NR1I3-related disorder	ClinVar	Detail
In this study, we investigated the effects of CYP2B6 516G>T (rs3745274), CYP2B6 c.485-18C>T (r...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs2307424 dbSNP
Genome: hg19
Position: chr1:161,202,605-161,202,605
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1204
Mean of sample read depth (HGVD): 132.16
Standard deviation of sample read depth (HGVD): 62.51
Number of reference allele (HGVD): 1118
Number of alternative allele (HGVD): 1289
Allele Frequency (HGVD): 0.5355213959285418
Gene Symbol (HGVD): NR1I3
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs2307424
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.5348
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 8962
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16758
East Asian Chromosome Counts (ExAC): 8634
East Asian Allele Counts (ExAC): 4630
East Asian Heterozygous Counts (ExAC): 2106
East Asian Homozygous Counts (ExAC): 1262
East Asian Allele Frequency (ExAC): 0.5362520268705119
Chromosome Counts in All Race (ExAC): 121348
Allele Counts in All Race (ExAC): 42888
Heterozygous Counts in All Race (ExAC): 26544
Homozygous Counts in All Race (ExAC): 8172
Allele Frequency in All Race (ExAC): 0.3534298051883838

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