GeneBe

ENST00000537545.1:n.144+835C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000537545.1(ADIPOR2):​n.144+835C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,970 control chromosomes in the GnomAD database, including 13,870 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 13870 hom., cov: 32)

Consequence

ADIPOR2
ENST00000537545.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0220

Publications

4 publications found
Variant links:
Genes affected
ADIPOR2 (HGNC:24041): (adiponectin receptor 2) The adiponectin receptors, ADIPOR1 (MIM 607945) and ADIPOR2, serve as receptors for globular and full-length adiponectin (MIM 605441) and mediate increased AMPK (see MIM 602739) and PPAR-alpha (PPARA; MIM 170998) ligand activities, as well as fatty acid oxidation and glucose uptake by adiponectin (Yamauchi et al., 2003 [PubMed 12802337]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 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
ADIPOR2ENST00000537545.1 linkn.144+835C>T intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.395
AC:
59931
AN:
151850
Hom.:
13868
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.147
Gnomad AMI
AF:
0.611
Gnomad AMR
AF:
0.362
Gnomad ASJ
AF:
0.468
Gnomad EAS
AF:
0.398
Gnomad SAS
AF:
0.421
Gnomad FIN
AF:
0.515
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.526
Gnomad OTH
AF:
0.378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.394
AC:
59939
AN:
151970
Hom.:
13870
Cov.:
32
AF XY:
0.394
AC XY:
29231
AN XY:
74250
show subpopulations
African (AFR)
AF:
0.147
AC:
6078
AN:
41454
American (AMR)
AF:
0.362
AC:
5517
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.468
AC:
1626
AN:
3472
East Asian (EAS)
AF:
0.399
AC:
2059
AN:
5166
South Asian (SAS)
AF:
0.421
AC:
2027
AN:
4810
European-Finnish (FIN)
AF:
0.515
AC:
5427
AN:
10538
Middle Eastern (MID)
AF:
0.405
AC:
119
AN:
294
European-Non Finnish (NFE)
AF:
0.526
AC:
35735
AN:
67960
Other (OTH)
AF:
0.377
AC:
795
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1685
3370
5054
6739
8424
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
578
1156
1734
2312
2890
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.461
Hom.:
6248
Bravo
AF:
0.371
Asia WGS
AF:
0.377
AC:
1316
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.48
DANN
Benign
0.41
PhyloP100
-0.022

Splicing

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

Publications

Other links and lift over

dbSNP: rs10773980; hg19: chr12-1798718; API