rs7138803

chr12-49853685-G-Achr12-49853685-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;