rs16928751

Positions:

• chr12-1781033-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024551.3(ADIPOR2):​c.795G>A​(p.Gln265=) variant causes a synonymous change. The variant allele was found at a frequency of 0.12 in 1,612,452 control chromosomes in the GnomAD database, including 12,452 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 0.14 (1575 hom., cov: 32)
  • Exomes 𝑓: 0.12 (10877 hom.)
• Consequence: ADIPOR2 NM_024551.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.87

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=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.795G>A	p.Gln265=	synonymous_variant	6/8	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.795G>A	p.Gln265=	synonymous_variant	6/8	1	NM_024551.3	ENSP00000349616	P1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20610 AN: 152020 Hom.: 1574 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0906

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.132

GnomAD3 exomes AF: 0.105 AC: 26285 AN: 249718 Hom.: 1637 AF XY: 0.104 AC XY: 14078 AN XY: 135034

Gnomad AFR exome AF: 0.205

Gnomad AMR exome AF: 0.0572

Gnomad ASJ exome AF: 0.0963

Gnomad EAS exome AF: 0.0270

Gnomad SAS exome AF: 0.0752

Gnomad FIN exome AF: 0.0986

Gnomad NFE exome AF: 0.128

Gnomad OTH exome AF: 0.109

GnomAD4 exome AF: 0.118 AC: 172925 AN: 1460312 Hom.: 10877 Cov.: 32 AF XY: 0.117 AC XY: 85001 AN XY: 726478

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.0599

Gnomad4 ASJ exome AF: 0.0953

Gnomad4 EAS exome AF: 0.0155

Gnomad4 SAS exome AF: 0.0755

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.136 AC: 20623 AN: 152140 Hom.: 1575 Cov.: 32 AF XY: 0.132 AC XY: 9804 AN XY: 74366

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0906

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.130

Alfa AF: 0.133 Hom.: 846

Bravo AF: 0.138

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.4
DANN	Benign	0.73

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: rs16928751; hg19: chr12-1890199; COSMIC: COSV63947904; COSMIC: COSV63947904;