Example: Gene HNF1B , Rsid rs41290504, Variant 10:101639877-A-C, Phenotype BMI and SMYD4

Variant 10:101293035-C-A

Frequency of variant in various dataset

Gen Kuwaiti population

AC = -

AN = -

Alt.AF = 0.477

GWAS-Imputed

Cardio-Metabo

Gen Kuwaiti population

AC = -

AN = -

Alt.AF = 0.495

GWAS-Imputed

OmniExpress

Gen. Kuwaiti population

AC = 461

AN = 928

Alt.AF = 0.497

Exome

Type 2 diabetes

AC = 124

AN = 228

Alt.AF = 0.544

Exome

Type 1 diabetes

AC = 57

AN = 126

Alt.AF = 0.452

Exome

MODY

AC = 40

AN = 94

Alt.AF = 0.426

Exome

Kuwait sub population frequency

Sub Population	Allele Count	Allele Number	Allele Frequency
Saudi	98	218	0.4500
Persian	132	250	0.5280
Bedouin	45	68	0.6620

Associations with phenotypes in local Kuwaiti population

Variant	Phenotype	Effect Size	P-Value	Transformation	Chip Type
10:101293035-C-A	logHbA1C	-0.1236	0.0141	INV	OmniExpress
10:101293035-C-A	logHbA1C	-0.0186	0.0099	RAW	OmniExpress

The direction of the regression coefficient represents the effect of minor allele in the sample

Summary

Chromosome :

Position :

101293035

Reference Allele :

Alternative Allele :

Clinical Significance :

p.A49A

RS ID :

rs41290504

Gene Info

Gene Name :

NKX2-3

Ensemble ID :

Gene Region :

Exonic

Exonic Function :

Consequence :

synonymous SNV

Prediction

Sift :

LRT :

Mutation Taster :

Mutation Assessor :

FATHMM :

FATHMM-MKL:

FATHMM XF Coding :

Global Frequency

gnomAD :

0.5368

EXAC :

0.5375

GME AF :

0.4491

GME NWA :

0.4596

GME NEA :

0.4334

GME AP :

0.3596

GME Israel :

0.6000

GME SD :

0.5172

GME TP :

0.4421

GME CA :

0.5417

Associated Traits

External links

Ensembl :

Click here to search the variant in Ensembl

dbSNP :

Click here to search the variant in dbSNP

UCSC :

Click here to search the variant in UCSC

ClinVar :

Click here to search the variant in ClinVar