12-49853685-G-A

Variant names:

• chr12-49853685-G-A
• rs7138803

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 316 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.170 AC: 7077 AN: 41540

American (AMR) AF: 0.264 AC: 4040 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1427 AN: 5172

South Asian (SAS) AF: 0.379 AC: 1829 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4004 AN: 10540

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25912 AN: 67966

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.356 Hom.: 46571

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

Dec 26, 2019

Department of Endocrinology, The Second Hospital of Jilin University

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: clinical testing

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.0
DANN	Benign	0.88
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7138803; hg19: chr12-50247468;