12-1722080-A-G

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-87+30889A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,110 control chromosomes in the GnomAD database, including 26,698 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 0.56 ( 26698 hom., cov: 32)

Consequence

ADIPOR2
NM_024551.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.515
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADIPOR2NM_024551.3 linkc.-87+30889A>G intron_variant Intron 1 of 7 ENST00000357103.5 NP_078827.2 Q86V24

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADIPOR2ENST00000357103.5 linkc.-87+30889A>G intron_variant Intron 1 of 7 1 NM_024551.3 ENSP00000349616.4 Q86V24
ADIPOR2ENST00000537545.1 linkn.145-32178A>G intron_variant Intron 1 of 2 3
ADIPOR2ENST00000540974.1 linkn.149-8645A>G intron_variant Intron 2 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.562
AC:
85452
AN:
151992
Hom.:
26697
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.266
Gnomad AMI
AF:
0.751
Gnomad AMR
AF:
0.623
Gnomad ASJ
AF:
0.615
Gnomad EAS
AF:
0.588
Gnomad SAS
AF:
0.595
Gnomad FIN
AF:
0.782
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.685
Gnomad OTH
AF:
0.553
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.562
AC:
85470
AN:
152110
Hom.:
26698
Cov.:
32
AF XY:
0.567
AC XY:
42166
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.266
Gnomad4 AMR
AF:
0.623
Gnomad4 ASJ
AF:
0.615
Gnomad4 EAS
AF:
0.589
Gnomad4 SAS
AF:
0.595
Gnomad4 FIN
AF:
0.782
Gnomad4 NFE
AF:
0.685
Gnomad4 OTH
AF:
0.553
Alfa
AF:
0.647
Hom.:
28551
Bravo
AF:
0.536
Asia WGS
AF:
0.565
AC:
1967
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.1
DANN
Benign
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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: rs10773983; hg19: chr12-1831246; API