rs35854772

chr12-1783911-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4 BP7 BA1

The NM_024551.3(ADIPOR2):c.870C>A(p.Ile290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,610,708 control chromosomes in the GnomAD database, including 12,291 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 0.13 (1511 hom., cov: 32)
  • Exomes 𝑓: 0.12 (10780 hom.)
• Consequence: ADIPOR2 NM_024551.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BP7: Synonymous conserved (PhyloP=1.66 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR2	NM_024551.3	c.870C>A	p.Ile290=	synonymous_variant	7/8	ENST00000357103.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.870C>A	p.Ile290=	synonymous_variant	7/8	1	NM_024551.3	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20255 AN: 151856 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0906

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.130

GnomAD3 exomes AF: 0.104 AC: 25945 AN: 248962 Hom.: 1594 AF XY: 0.103 AC XY: 13886 AN XY: 134584

Gnomad AFR exome AF: 0.197

Gnomad AMR exome AF: 0.0566

Gnomad ASJ exome AF: 0.0956

Gnomad EAS exome AF: 0.0266

Gnomad SAS exome AF: 0.0746

Gnomad FIN exome AF: 0.0984

Gnomad NFE exome AF: 0.128

Gnomad OTH exome AF: 0.107

GnomAD4 exome AF: 0.118 AC: 172012 AN: 1458734 Hom.: 10780 Cov.: 31 AF XY: 0.117 AC XY: 84573 AN XY: 725702

Gnomad4 AFR exome AF: 0.198

Gnomad4 AMR exome AF: 0.0593

Gnomad4 ASJ exome AF: 0.0951

Gnomad4 EAS exome AF: 0.0155

Gnomad4 SAS exome AF: 0.0753

Gnomad4 FIN exome AF: 0.102

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.133 AC: 20265 AN: 151974 Hom.: 1511 Cov.: 32 AF XY: 0.130 AC XY: 9655 AN XY: 74312

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0906

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.0988

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.128

Alfa AF: 0.131 Hom.: 605

Bravo AF: 0.135

Asia WGS AF: 0.0520 AC: 183 AN: 3478

EpiCase AF: 0.126

EpiControl AF: 0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
Cadd	Benign	10
Dann	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs35854772; hg19: chr12-1893077; COSMIC: COSV63945824; COSMIC: COSV63945824;