chr16:28883241:A>G Detail (hg19) (SH2B1)

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

Information

Genome

Assembly	Position
hg19	chr16:28,883,241-28,883,241
hg38	chr16:28,871,920-28,871,920 View the variant detail on this assembly version.

HGVS

SH2B1

Type	Transcript	Protein
RefSeq	NM_001308293.1:c.1450A>G	NP_001295222.1:p.Thr484Ala
	NM_001308294.1:c.442A>G	NP_001295223.1:p.Thr148Ala
	NM_001145795.1:c.1450A>G	NP_001139267.1:p.Thr484Ala
	NM_001145812.1:c.1450A>G	NP_001139284.1:p.Thr484Ala
	NM_015503.2:c.1450A>G	NP_056318.2:p.Thr484Ala
Ensemble	ENST00000322610.12:c.1450A>G	ENST00000322610.12:p.Thr484Ala
	ENST00000684370.1:c.1450A>G	ENST00000684370.1:p.Thr484Ala
	ENST00000538342.5:c.442A>G	ENST00000538342.5:p.Thr148Ala
	ENST00000618521.4:c.1450A>G	ENST00000618521.4:p.Thr484Ala
	ENST00000395532.8:c.1450A>G	ENST00000395532.8:p.Thr484Ala
	ENST00000707128.1:c.1450A>G	ENST00000707128.1:p.Thr484Ala
	ENST00000337120.9:c.1450A>G	ENST00000337120.9:p.Thr484Ala

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.151
	ToMMo:0.147
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.109

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

SH2B1

Type	Database	ID	Link
Gene	MIM	608937	OMIM
	HGNC	30417	HGNC
	Ensembl	ENSG00000178188	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv55190363	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2024-01-31	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.003	obesity	Carriers of obesity risk alleles of non-synonymous SNPs in SH2B1 (rs7498665, Thr...	BeFree	23519644	Detail
0.231	obesity	Carriers of obesity risk alleles of non-synonymous SNPs in SH2B1 (rs7498665, Thr...	BeFree	23519644	Detail
<0.001	obesity	Analyses of non-synonymous obesity risk alleles in SH2B1 (rs7498665) and APOB48R...	BeFree	23519644	Detail
0.278	obesity	Analyses of non-synonymous obesity risk alleles in SH2B1 (rs7498665) and APOB48R...	BeFree	23519644	Detail
0.278	obesity	Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and p...	GWASCAT	23563607	Detail
0.278	obesity	The nominal associations of rs925946 and rs7498665 obesity risk variants near th...	BeFree	23640704	Detail
0.278	obesity	Replication of the SH2B1 rs7498665 association with obesity in a Belgian study p...	BeFree	22248999	Detail
0.011	Diabetes Mellitus, Non-Insulin-Dependent	SH2B1 rs7498665 associated with type 2 diabetes independently of BMI.	BeFree	21912638	Detail
0.155	obesity	Five other SNPs (SH2B1 rs7498665, MTCH2 rs4752856, MC4R rs17782313, NEGR1 rs2815...	BeFree	19164386	Detail
0.011	Diabetes Mellitus, Non-Insulin-Dependent	In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observ...	BeFree	24528214	Detail
0.153	obesity	Five other SNPs (SH2B1 rs7498665, MTCH2 rs4752856, MC4R rs17782313, NEGR1 rs2815...	BeFree	19164386	Detail
0.791	obesity	Five other SNPs (SH2B1 rs7498665, MTCH2 rs4752856, MC4R rs17782313, NEGR1 rs2815...	BeFree	19164386	Detail
0.341	Diabetes Mellitus, Non-Insulin-Dependent	In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observ...	BeFree	24528214	Detail
0.155	obesity	In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observ...	BeFree	24528214	Detail
0.007	Diabetes Mellitus, Non-Insulin-Dependent	In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observ...	BeFree	24528214	Detail
0.278	obesity	In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observ...	BeFree	24528214	Detail

Annotation

Annotations

Descrption	Source	Links
NM_001387430.1(SH2B1):c.1450A>G (p.Thr484Ala) AND not provided	ClinVar	Detail
Carriers of obesity risk alleles of non-synonymous SNPs in SH2B1 (rs7498665, Thr484Ala) or APOB48R (...	DisGeNET	Detail
Carriers of obesity risk alleles of non-synonymous SNPs in SH2B1 (rs7498665, Thr484Ala) or APOB48R (...	DisGeNET	Detail
Analyses of non-synonymous obesity risk alleles in SH2B1 (rs7498665) and APOB48R (rs180743) in obese...	DisGeNET	Detail
Analyses of non-synonymous obesity risk alleles in SH2B1 (rs7498665) and APOB48R (rs180743) in obese...	DisGeNET	Detail
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights int...	DisGeNET	Detail
The nominal associations of rs925946 and rs7498665 obesity risk variants near the BDNF and SH2B1 gen...	DisGeNET	Detail
Replication of the SH2B1 rs7498665 association with obesity in a Belgian study population.	DisGeNET	Detail
SH2B1 rs7498665 associated with type 2 diabetes independently of BMI.	DisGeNET	Detail
Five other SNPs (SH2B1 rs7498665, MTCH2 rs4752856, MC4R rs17782313, NEGR1 rs2815752 and GNPDA2 rs109...	DisGeNET	Detail
In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observed a statistically s...	DisGeNET	Detail
Five other SNPs (SH2B1 rs7498665, MTCH2 rs4752856, MC4R rs17782313, NEGR1 rs2815752 and GNPDA2 rs109...	DisGeNET	Detail
Five other SNPs (SH2B1 rs7498665, MTCH2 rs4752856, MC4R rs17782313, NEGR1 rs2815752 and GNPDA2 rs109...	DisGeNET	Detail
In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observed a statistically s...	DisGeNET	Detail
In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observed a statistically s...	DisGeNET	Detail
In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observed a statistically s...	DisGeNET	Detail
In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observed a statistically s...	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: rs7498665 dbSNP
Genome: hg19
Position: chr16:28,883,241-28,883,241
Variant Type: snv
Reference Allele: A
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 1194
Mean of sample read depth (HGVD): 66.70
Standard deviation of sample read depth (HGVD): 32.84
Number of reference allele (HGVD): 2028
Number of alternative allele (HGVD): 360
Allele Frequency (HGVD): 0.1507537688442211
Gene Symbol (HGVD): SH2B1
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)): rs7498665
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.1465
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 2453
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16748
East Asian Chromosome Counts (ExAC): 8626
East Asian Allele Counts (ExAC): 937
East Asian Heterozygous Counts (ExAC): 807
East Asian Homozygous Counts (ExAC): 65
East Asian Allele Frequency (ExAC): 0.10862508694644099
Chromosome Counts in All Race (ExAC): 121258
Allele Counts in All Race (ExAC): 41869
Heterozygous Counts in All Race (ExAC): 25765
Homozygous Counts in All Race (ExAC): 8052
Allele Frequency in All Race (ExAC): 0.34528855828069077

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