rs7138803

Positions:

• chr12-49853685-G-A
• chr12-49853685-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.309 in 152,112 control chromosomes in the GnomAD database, including 8,048 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.31 (8048 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47070 AN: 151994 Hom.: 8048 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.309

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 47059 AN: 152112 Hom.: 8048 Cov.: 33 AF XY: 0.308 AC XY: 22935 AN XY: 74344

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.306

Alfa AF: 0.364 Hom.: 24464

Bravo AF: 0.290

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Obesity Other:1

risk factor, no assertion criteria provided

clinical testing

Department of Endocrinology, The Second Hospital of Jilin University

Dec 26, 2019

We found that loci may be associated with obesity-related indicators, and may increase susceptibility of concurrent type 2 diabetes associated with obesity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.0
DANN	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7138803; hg19: chr12-50247468;