rs6548238

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -1.90
Variant links:

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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 rank MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.852
AC:
129546
AN:
152006
Hom.:
55318
Cov.:
31
show subpopulations
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
show subpopulations
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
LINK: link

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 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6548238; hg19: chr2-634905; API