chr17:7536527:G>A Detail (hg19) (SHBG)

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

Genome

Assembly	Position
hg19	chr17:7,536,527-7,536,527
hg38	chr17:7,633,209-7,633,209 View the variant detail on this assembly version.

HGVS

SHBG

Type	Transcript	Protein
RefSeq	NM_001146280.2:c.858G>A	NP_001139752.1:p.Lys286=
	NM_001040.4:c.1066G>A	NP_001031.2:p.Asp356Asn
	NM_001289116.1:c.1066G>A	NP_001276045.1:p.Asp356Asn
	NM_001289113.1:c.892G>A	NP_001276042.1:p.Asp298Asn
	NM_001289115.1:c.892G>A	NP_001276044.1:p.Asp298Asn
	NM_001289114.1:c.892G>A	NP_001276043.1:p.Asp298Asn
	NM_001146279.2:c.1012G>A	NP_001139751.1:p.Asp338Asn
	NM_001146281.2:c.721G>A	NP_001139753.1:p.Asp241Asn
Ensemble	ENST00000570547.5:c.547G>A	ENST00000570547.5:p.Asp183Asn
	ENST00000416273.7:c.858G>A	ENST00000416273.7:p.Lys286=
	ENST00000380450.9:c.1066G>A	ENST00000380450.9:p.Asp356Asn
	ENST00000572182.5:c.225G>A	ENST00000572182.5:p.Lys75=
	ENST00000572262.5:c.730G>A	ENST00000572262.5:p.Asp244Asn
	ENST00000340624.9:c.892G>A	ENST00000340624.9:p.Asp298Asn
	ENST00000575314.5:c.892G>A	ENST00000575314.5:p.Asp298Asn
	ENST00000575903.5:c.1012G>A	ENST00000575903.5:p.Asp338Asn
	ENST00000574539.5:c.684G>A	ENST00000574539.5:p.Lys228=
	ENST00000576478.5:c.385G>A	ENST00000576478.5:p.Asp129Asn
	ENST00000441599.6:c.721G>A	ENST00000441599.6:p.Asp241Asn
	ENST00000576728.5:c.522G>A	ENST00000576728.5:p.Lys174=

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.093
	ToMMo:0.108
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.117

Prediction

ClinVar

Clinical Significance	Benign
Review star
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Links

SHBG

Type	Database	ID	Link
Gene	MIM	182205	OMIM
	HGNC	10839	HGNC
	Ensembl	ENSG00000129214	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv56955016	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2020-06-23	criteria provided, single submitter	not provided	germline	Detail
Benign	2019-11-04	criteria provided, single submitter	SHBG-related disorder	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.033	breast carcinoma	We did not observe an association between potential functional genetic polymorph...	BeFree	23935996	Detail
0.114	Malignant neoplasm of breast	We did not observe an association between potential functional genetic polymorph...	BeFree	23935996	Detail
0.004	breast carcinoma	We did not observe an association between potential functional genetic polymorph...	BeFree	23935996	Detail
0.080	breast carcinoma	We did not observe an association between potential functional genetic polymorph...	BeFree	23935996	Detail
0.028	Malignant neoplasm of breast	We did not observe an association between potential functional genetic polymorph...	BeFree	23935996	Detail
0.132	Malignant neoplasm of breast	We did not observe an association between potential functional genetic polymorph...	BeFree	23935996	Detail
0.023	Malignant neoplasm of breast	Implications of gene-environment interaction in studies of gene variants in brea...	BeFree	16982738	Detail
0.008	breast carcinoma	Implications of gene-environment interaction in studies of gene variants in brea...	BeFree	16982738	Detail
0.023	Malignant neoplasm of breast	Further, the relation between breast cancer risk and SHBG rs6259 was found to va...	BeFree	21454829	Detail
0.008	breast carcinoma	Association between SHBG Asp327Asn (rs6259) polymorphism and breast cancer risk:...	BeFree	22711300	Detail
<0.001	gallbladder carcinoma	Among women taking oral contraceptives, the effect of SHBG Ex8 + 6 (rs6259) on g...	BeFree	19168589	Detail
0.023	Malignant neoplasm of breast	Association between SHBG Asp327Asn (rs6259) polymorphism and breast cancer risk:...	BeFree	22711300	Detail
0.008	breast carcinoma	Further, the relation between breast cancer risk and SHBG rs6259 was found to va...	BeFree	21454829	Detail
<0.001	Malignant neoplasm of gallbladder	Among women taking oral contraceptives, the effect of SHBG Ex8 + 6 (rs6259) on g...	BeFree	19168589	Detail
0.019	breast carcinoma	Five SNPs (AHR rs2066853, ATM rs1003623, ESR1 rs2234693, GSTP1 rs1695, and SHBG ...	BeFree	21454829	Detail
0.099	Malignant neoplasm of breast	Five SNPs (AHR rs2066853, ATM rs1003623, ESR1 rs2234693, GSTP1 rs1695, and SHBG ...	BeFree	21454829	Detail

Annotation

Annotations

Descrption	Source	Links
NM_001040.5(SHBG):c.1066G>A (p.Asp356Asn) AND not provided	ClinVar	Detail
NM_001040.5(SHBG):c.1066G>A (p.Asp356Asn) AND SHBG-related disorder	ClinVar	Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen...	DisGeNET	Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen...	DisGeNET	Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen...	DisGeNET	Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen...	DisGeNET	Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen...	DisGeNET	Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen...	DisGeNET	Detail
Implications of gene-environment interaction in studies of gene variants in breast cancer: an exampl...	DisGeNET	Detail
Implications of gene-environment interaction in studies of gene variants in breast cancer: an exampl...	DisGeNET	Detail
Further, the relation between breast cancer risk and SHBG rs6259 was found to vary by body mass inde...	DisGeNET	Detail
Association between SHBG Asp327Asn (rs6259) polymorphism and breast cancer risk: a meta-analysis of ...	DisGeNET	Detail
Among women taking oral contraceptives, the effect of SHBG Ex8 + 6 (rs6259) on gallbladder cancer (O...	DisGeNET	Detail
Association between SHBG Asp327Asn (rs6259) polymorphism and breast cancer risk: a meta-analysis of ...	DisGeNET	Detail
Further, the relation between breast cancer risk and SHBG rs6259 was found to vary by body mass inde...	DisGeNET	Detail
Among women taking oral contraceptives, the effect of SHBG Ex8 + 6 (rs6259) on gallbladder cancer (O...	DisGeNET	Detail
Five SNPs (AHR rs2066853, ATM rs1003623, ESR1 rs2234693, GSTP1 rs1695, and SHBG rs6259) showed gener...	DisGeNET	Detail
Five SNPs (AHR rs2066853, ATM rs1003623, ESR1 rs2234693, GSTP1 rs1695, and SHBG rs6259) showed gener...	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: rs6259 dbSNP
Genome: hg19
Position: chr17:7,536,527-7,536,527
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1121
Mean of sample read depth (HGVD): 67.37
Standard deviation of sample read depth (HGVD): 31.68
Number of reference allele (HGVD): 2034
Number of alternative allele (HGVD): 208
Allele Frequency (HGVD): 0.0927743086529884
Gene Symbol (HGVD): SHBG
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)): rs6259
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.1082
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 1814
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8646
East Asian Allele Counts (ExAC): 1012
East Asian Heterozygous Counts (ExAC): 884
East Asian Homozygous Counts (ExAC): 64
East Asian Allele Frequency (ExAC): 0.11704834605597965
Chromosome Counts in All Race (ExAC): 121400
Allele Counts in All Race (ExAC): 10918
Heterozygous Counts in All Race (ExAC): 9616
Homozygous Counts in All Race (ExAC): 651
Allele Frequency in All Race (ExAC): 0.08993410214168039

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