rs35854772

Variant names:

• chr12-1783911-C-A
• rs35854772
• NM_024551.3:c.870C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4 BP7 BA1

The NM_024551.3(ADIPOR2):​c.870C>A​(p.Ile290Ile) 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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.870C>A	p.Ile290Ile	synonymous	Exon 7 of 8	NP_078827.2
	ADIPOR2	NM_001375363.1		c.969C>A	p.Ile323Ile	synonymous	Exon 8 of 9	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.870C>A	p.Ile290Ile	synonymous	Exon 8 of 9	NP_001362293.1	Q86V24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.870C>A	p.Ile290Ile	synonymous	Exon 7 of 8	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.1053C>A	p.Ile351Ile	synonymous	Exon 9 of 10	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.975C>A	p.Ile325Ile	synonymous	Exon 8 of 9	ENSP00000549023.1

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

GnomAD2 exomes AF: 0.104 AC: 25945 AN: 248962 AF XY: 0.103

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 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

African (AFR) AF: 0.198 AC: 6594 AN: 33320

American (AMR) AF: 0.0593 AC: 2631 AN: 44378

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 2469 AN: 25958

East Asian (EAS) AF: 0.0155 AC: 613 AN: 39642

South Asian (SAS) AF: 0.0753 AC: 6465 AN: 85886

European-Finnish (FIN) AF: 0.102 AC: 5468 AN: 53358

Middle Eastern (MID) AF: 0.0924 AC: 532 AN: 5760

European-Non Finnish (NFE) AF: 0.127 AC: 140705 AN: 1110126

Other (OTH) AF: 0.108 AC: 6535 AN: 60306

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

African (AFR) AF: 0.194 AC: 8048 AN: 41416

American (AMR) AF: 0.0841 AC: 1283 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0906 AC: 314 AN: 3466

East Asian (EAS) AF: 0.0244 AC: 126 AN: 5174

South Asian (SAS) AF: 0.0746 AC: 357 AN: 4788

European-Finnish (FIN) AF: 0.0988 AC: 1046 AN: 10586

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8770 AN: 67968

Other (OTH) AF: 0.128 AC: 270 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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