NM_024551.3:c.795G>A

Variant names:

• chr12-1781033-G-A
• rs16928751
• NM_024551.3:c.795G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024551.3(ADIPOR2):​c.795G>A​(p.Gln265Gln) 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
• Publications: 37 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=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 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.795G>A	p.Gln265Gln	synonymous	Exon 6 of 8	NP_078827.2
	ADIPOR2	NM_001375363.1		c.795G>A	p.Gln265Gln	synonymous	Exon 6 of 9	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.795G>A	p.Gln265Gln	synonymous	Exon 7 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.795G>A	p.Gln265Gln	synonymous	Exon 6 of 8	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.873G>A	p.Gln291Gln	synonymous	Exon 7 of 10	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.795G>A	p.Gln265Gln	synonymous	Exon 6 of 9	ENSP00000549023.1

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

GnomAD2 exomes AF: 0.105 AC: 26285 AN: 249718 AF XY: 0.104

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 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

African (AFR) AF: 0.206 AC: 6881 AN: 33398

American (AMR) AF: 0.0599 AC: 2659 AN: 44374

Ashkenazi Jewish (ASJ) AF: 0.0953 AC: 2489 AN: 26108

East Asian (EAS) AF: 0.0155 AC: 615 AN: 39612

South Asian (SAS) AF: 0.0755 AC: 6492 AN: 85968

European-Finnish (FIN) AF: 0.103 AC: 5474 AN: 53398

Middle Eastern (MID) AF: 0.0935 AC: 539 AN: 5764

European-Non Finnish (NFE) AF: 0.127 AC: 141197 AN: 1111368

Other (OTH) AF: 0.109 AC: 6579 AN: 60322

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

African (AFR) AF: 0.202 AC: 8377 AN: 41490

American (AMR) AF: 0.0847 AC: 1295 AN: 15282

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

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5180

South Asian (SAS) AF: 0.0749 AC: 361 AN: 4822

European-Finnish (FIN) AF: 0.0990 AC: 1047 AN: 10576

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

European-Non Finnish (NFE) AF: 0.129 AC: 8778 AN: 68006

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.131 Hom.: 1067

Bravo AF: 0.138

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.4
DANN	Benign	0.73
PhyloP100		3.9
Mutation Taster		=96/4	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: rs16928751; hg19: chr12-1890199; COSMIC: COSV63947904; COSMIC: COSV63947904;