rs6548238

chr2-634905-T-Cchr2-634905-T-G

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 0.852 in 152,124 control chromosomes in the GnomAD database, including 55,361 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 0.85 (55361 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.852 AC: 129546 AN: 152006 Hom.: 55318 Cov.: 31

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.852 AC: 129646 AN: 152124 Hom.: 55361 Cov.: 31 AF XY: 0.855 AC XY: 63550 AN XY: 74350

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.845

Alfa AF: 0.833 Hom.: 67606

Bravo AF: 0.854

Asia WGS AF: 0.894 AC: 3110 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 near TMEM18 (rs6548238) 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	-0.86
Cadd	Benign	1.1
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6548238; hg19: chr2-634905;