dbSNP rs9805042: ADIPOR2:p.Tyr321Tyr (chr12-1784004-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_024551.3(ADIPOR2):c.963C>T(p.Tyr321Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,613,196 control chromosomes in the GnomAD database, including 21,924 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 0.22 ( 5732 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16192 hom. )

Consequence

ADIPOR2
NM_024551.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.177

Publications

13 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP7

Synonymous conserved (PhyloP=0.177 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3 link	c.963C>T	p.Tyr321Tyr	synonymous_variant	Exon 7 of 8	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5 link	c.963C>T	p.Tyr321Tyr	synonymous_variant	Exon 7 of 8	1	NM_024551.3	ENSP00000349616.4

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34067

AN:

151986

Hom.:

5720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.208

GnomAD2 exomes

AF:

0.144

AC:

36042

AN:

250636

AF XY:

0.140

show subpopulations

Gnomad AFR exome

AF:

0.484

Gnomad AMR exome

AF:

0.0785

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.0930

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.132

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.136

AC:

199069

AN:

1461092

Hom.:

16192

Cov.:

AF XY:

0.136

AC XY:

98495

AN XY:

726844

show subpopulations

African (AFR)

AF:

0.487

AC:

16270

AN:

33414

American (AMR)

AF:

0.0835

AC:

3729

AN:

44674

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

3400

AN:

26108

East Asian (EAS)

AF:

0.0740

AC:

2936

AN:

39684

South Asian (SAS)

AF:

0.145

AC:

12470

AN:

86128

European-Finnish (FIN)

AF:

0.105

AC:

5626

AN:

53406

Middle Eastern (MID)

AF:

0.139

AC:

800

AN:

5766

European-Non Finnish (NFE)

AF:

0.130

AC:

144779

AN:

1111546

Other (OTH)

AF:

0.150

AC:

9059

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

9455

18911

28366

37822

47277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5356

10712

16068

21424

26780

<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:

0.224

AC:

34117

AN:

152104

Hom.:

5732

Cov.:

AF XY:

0.221

AC XY:

16403

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.475

AC:

19704

AN:

41444

American (AMR)

AF:

0.128

AC:

1964

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

452

AN:

3472

East Asian (EAS)

AF:

0.104

AC:

537

AN:

5168

South Asian (SAS)

AF:

0.157

AC:

757

AN:

4820

European-Finnish (FIN)

AF:

0.102

AC:

1078

AN:

10588

Middle Eastern (MID)

AF:

0.137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.134

AC:

9121

AN:

68004

Other (OTH)

AF:

0.207

AC:

437

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1162

2325

3487

4650

5812

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.178

Hom.:

2588

Bravo

AF:

0.235

Asia WGS

AF:

0.160

AC:

556

AN:

3478

EpiCase

AF:

0.133

EpiControl

AF:

0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

5.6

(source)

DANN

Benign

0.58

PhyloP100

0.18

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=96/4

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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