Genetic Variant ADIPOR2:p.Gln265Gln (chr12-1781033-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.87

Publications

37 publications found

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]

ADIPOR2 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3 link	c.795G>A	p.Gln265Gln	synonymous_variant	Exon 6 of 8	ENST00000357103.5	NP_078827.2	Q86V24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5 link	c.795G>A	p.Gln265Gln	synonymous_variant	Exon 6 of 8	1	NM_024551.3	ENSP00000349616.4		Q86V24
ADIPOR2	ENST00000537190.1 link	n.*66G>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20610

AN:

152020

Hom.:

1574

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.117

AC XY:

85001

AN XY:

726478

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

8071

16141

24212

32282

40353

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5036

10072

15108

20144

25180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.136

AC:

20623

AN:

152140

Hom.:

1575

Cov.:

AF XY:

0.132

AC XY:

9804

AN XY:

74366

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8778

AN:

68006

Other (OTH)

AF:

0.130

AC:

274

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

899

1797

2696

3594

4493

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

9.4

(source)

DANN

Benign

0.73

PhyloP100

3.9

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over